METHODS AND COMPOSITIONS FOR MODULATING A GENOME

Abstract

Methods and compositions for modulating a target genome are disclosed. The composition may comprise a first RNA encoding a polypeptide comprising a retrotransposase reverse transcriptase domain and a retrotransposase endonuclease domain. The composition may also comprise a second RNA comprising a sequence that binds the polypeptide and a heterologous object sequence. The composition may insert the sequence of the heterologous object sequence into a target DNA.

Description

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on May 16, 2024, is named V2065-700040_SL.xml and is 3,505,256 bytes in size.

BACKGROUND

Integration of a nucleic acid of interest into a genome occurs at low frequency and with little site specificity, in the absence of a specialized protein to promote the insertion event. Some existing approaches, like CRISPR/Cas9, are more suited for small edits and are less effective at integrating longer sequences. Other existing approaches, like Cre/loxP, require a first step of inserting a loxP site into the genome and then a second step of inserting a sequence of interest into the loxP site. There is a need in the art for improved proteins for inserting sequences of interest into a genome.

SUMMARY OF THE INVENTION

This disclosure relates to novel compositions, systems and methods for altering a genome at one or more locations in a host cell, tissue or subject, in vivo or in vitro. In particular, the invention features compositions, systems and methods for the introduction of exogenous genetic elements into a host genome.

Features of the compositions or methods can include one or more of the following enumerated embodiments.

1. A system for modifying DNA comprising:

• • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence that encodes a therapeutic polypeptide or that encodes a mammalian (e.g., human) polypeptide, or a fragment or variant thereof.2. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence, wherein one or more of:
  • i. the heterologous object sequence encodes a protein, e.g. an enzyme (e.g., a lysosomal enzyme) or a blood factor (e.g., Factor I, II, V, VII, X, XI, XII or XIII);
  • ii. the heterologous object sequence comprises a tissue specific promoter or enhancer;
  • iii. the heterologous object sequence encodes a polypeptide of greater than 250, 300, 400, 500, or 1,000 amino acids, and optionally up to 7,500 amino acids;
  • iv. the heterologous object sequence encodes a fragment of a mammalian gene but does not encode the full mammalian gene, e.g., encodes one or more exons but does not encode a full-length protein;
  • v. the heterologous object sequence encodes one or more introns;
  • vi. the heterologous object sequence is other than a GFP, e.g., is other than a fluorescent protein or is other than a reporter protein.
  • vii. the heterologous object sequence is other than a T cell chimeric antigen receptor3. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.4. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a target DNA binding domain, (ii) a reverse transcriptase domain and (iii) an endonuclease domain; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.5. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain, wherein one or both of (i) or (ii) are derived from an avian retrotransposase, e.g., have a sequence of Table 2 or 3 or at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.6. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain, wherein the polypeptide has an activity at 37° C. that is no less than 70%, 75%, 80%, 85%, 90%, or 95% of its activity at 25° C. under otherwise similar conditions; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.7. The system of embodiment 6, wherein the polypeptide is derived from an avian retrotransposase, e.g., an avian retrotransposase of column 8 of Table 3, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.8. The system of embodiment 6, wherein the avian retrotransposase is a retrotransposase from Taeniopygia guttata, Geospiza fortis, Zonotrichia albicollis, or Tinamus guttatus, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.9. The system of embodiment 6, wherein the polypeptide is derived from a retrotransposase of column 8 of Table 3, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.10. The system of any of the preceding embodiments, wherein the template RNA comprises a sequence of Table 3 (e.g., one or both of a 5′ untranslated region of column 6 of Table 3 and a 3′ untranslated region of column 7 of Table 3), or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.11. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence, wherein one or more of:
  • i. the nucleic acid encoding the polypeptide and the template RNA or a nucleic acid encoding the template RNA are separate nucleic acids;
  • ii. the template RNA does not encode an active reverse transcriptase, e.g., comprises an inactivated mutant reverse transcriptase, e.g., as described in Examples 1-2, or does not comprise a reverse transcriptase sequence; or
  • iii. the template RNA does not encode an active endonuclease, e.g., comprises an inactivated endonuclease or does not comprise an endonuclease; or
  • iv. the template RNA comprises one or more chemical modifications.12. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a 5′ untranslated sequence that binds the polypeptide, (ii) a 3′ untranslated sequence that binds the polypeptide, (iii) a heterologous object sequence, and (iv) a promoter operably linked to the heterologous object sequence,
  • wherein the promoter is disposed between the 5′ untranslated sequence that binds the polypeptide and the heterologous sequence, or
  • wherein the promoter is disposed between the 3′ untranslated sequence that binds the polypeptide and the heterologous sequence.13. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a 5′ untranslated sequence that binds the polypeptide, (ii) a 3′ untranslated sequence that binds the polypeptide, and (iii) a heterologous object sequence, and
  • wherein the heterologous object sequence comprises an open reading frame (or the reverse complement thereof) in a 5′ to 3′ orientation on the template RNA; or
  • wherein the heterologous object sequence comprises an open reading frame (or the reverse complement thereof) in a 3′ to 5′ orientation on the template RNA.14. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain, wherein at least one of (i) or (ii) is heterologous, and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.15. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a target DNA binding domain, (i) a reverse transcriptase domain and (iii) an endonuclease domain, wherein at least one of (i), (ii) or (iii) is heterologous, and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.16. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a sequence at least 80% identical (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identical) to a reverse transcriptase domain of a purinic/apyrimidinic endonuclease (APE)-type non-LTR retrotransposon and (ii) a sequence at least 80% identical (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identical) to an endonuclease domain of an APE-type non-LTR retrotransposon; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.17. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a sequence at least 80% identical (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identical) to a reverse transcriptase domain of a restriction enzyme-like endonuclease (RLE)-type non-LTR retrotransposon, (ii) a sequence at least 80% identical (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identical) to an endonuclease domain of a RLE-type non-LTR retrotransposon, and (iii) a heterologous target DNA binding domain (e.g., a heterologous zinc-finger DNA binding domain); and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.18. The system of any of the preceding embodiments, wherein the template RNA comprises (iii) a promoter operably linked to the heterologous object sequence.19. The system of any of the preceding embodiments, wherein the polypeptide further comprises (iii) a DNA-binding domain.20. The system of embodiment 17, wherein the polypeptide comprises a sequence at least 80% identical (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identical) to the sequence of SEQ ID NO: 1016.21. The system of any of the preceding embodiments, wherein the polypeptide comprises a sequence at least 80% identical (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identical) to a sequence in column 8 of Table 3.22. The system of any of the preceding embodiments, wherein the nucleic acid encoding the polypeptide and the template RNA or the nucleic acid encoding the template RNA are covalently linked, e.g., are part of a fusion nucleic acid.23. The system of embodiment 22, wherein the fusion nucleic acid comprises RNA.24. The system of embodiment 22, wherein the fusion nucleic acid comprises DNA.25. The system of any of the preceding embodiments, wherein (b) comprises template RNA.26. The system of embodiment 25, wherein the template RNA further comprises a nuclear localization signal.27. The system of any of the preceding embodiments, wherein (a) comprises RNA encoding the polypeptide.28. The system of embodiment 27, wherein the RNA of (a) and the RNA of (b) are separate RNA molecules.29. The system of embodiment 28, wherein the RNA of (a) and the RNA of (b) are present at a ratio of between 10:1 and 5:1, 5:1 and 2:1, 2:1 and 1:1, 1:1 and 1:2, 1:2 and 1:5, or 1:5 and 1:10.30. The system of embodiment 28, wherein the RNA of (a) does not comprise a nuclear localization signal.31. The system of any of the preceding embodiments, wherein the polypeptide further comprises a nuclear localization signal and/or a nucleolar localization signal.32. The system of any of the preceding embodiments, wherein (a) comprises an RNA that encodes: (i) the polypeptide and (ii) a nuclear localization signal and/or a nucleolar localization signal.33. The system of any of the preceding embodiments, wherein the RNA comprises a pseudoknot sequence, e.g., 5′ of the heterologous object sequence.34. The system of embodiment 33, wherein the RNA comprises a stem-loop sequence or a helix, 5′ of the pseudoknot sequence.35. The system of embodiment 33 or 34, wherein the RNA comprises one or more (e.g., 2, 3, or more) stem-loop sequences or helices 3′ of the pseudoknot sequence, e.g. 3′ of the pseudoknot sequence and 5′ of the heterologous object sequence.36. The system of any of embodiments 33-35, wherein the template RNA comprising the pseudoknot has catalytic activity, e.g., RNA-cleaving activity, e.g, cis-RNA-cleaving activity.37. The system of any of the preceding embodiments, wherein the RNA comprises at least one stem-loop sequence or helix, e.g., 3′ of the heterologous object sequence, e.g. 1, 2, 3, 4, 5 or more stem-loop sequences, hairpins or helices sequences.38. Any above-numbered system, wherein the polypeptide comprises a sequence of at least 50 amino acids (e.g., at least 100, 150, 200, 300, 500 amino acids) having at least 80% identity (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identity) to a sequence of a polypeptide listed in Table 1, or a reverse transcriptase domain or endonuclease domain thereof.39. Any above-numbered system, wherein the polypeptide comprises a sequence of at least 50 amino acids (e.g., at least 100, 150, 200, 300, 500 amino acids) having at least 80% identity (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identity) to a sequence of a polypeptide listed in any of Tables 2-3 or a reverse transcriptase domain, endonuclease domain, or DNA binding domain thereof.40. Any above-numbered system, wherein the polypeptide comprises a sequence of at least 50 amino acids (e.g., at least 100, 150, 200, 300, 500 amino acids) having at least 80% identity (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identity) to the amino acid sequence of column 8 of Table 3, or a reverse transcriptase domain, endonuclease domain, or DNA binding domain thereof.41. Any above-numbered system, wherein the template RNA comprises a sequence of Table 3 (e.g., one or both of a 5′ untranslated region of column 6 of Table 3 and a 3′ untranslated region of column 7 of Table 3), or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.42. The system of embodiment 41, wherein the template RNA comprises a sequence of about 100-125 bp from a 3′ untranslated region of column 7 of Table 3, e.g., wherein the sequence comprises nucleotides 1-100, 101-200, or 201-325 of the 3′ untranslated region of column 7 of Table 3, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.43. Any above-numbered system, wherein (a) comprises RNA and (b) comprises RNA.44. Any above-numbered system, which comprises only RNA, or which comprises more RNA than DNA by an RNA:DNA ratio of at least 10:1, 20:1, 30:1, 40:1, 50:1, 60:1, 70:1, 80:1, 90:1, or 100:1.45. Any above-numbered system, which does not comprise DNA, or which does not comprise more than 10%, 5%, 4%, 3%, 2%, or 1% DNA by mass or by molar amount.46. Any above-numbered system, which is capable of modifying DNA by insertion of the heterologous object sequence without an intervening DNA-dependent RNA polymerization of (b).47. Any above-numbered system, which is capable of modifying DNA by insertion of a heterologous object sequence in the presence of an inhibitor of a DNA repair pathway (e.g., SCR7, a PARP inhibitor), or in a cell line deficient for a DNA repair pathway (e.g., a cell line deficient for the nucleotide excision repair pathway or the homology-directed repair pathway).48. Any above-numbered system, which does not cause formation of a detectable level of double stranded breaks in a target cell.49. Any above-numbered system, which is capable of modifying DNA using reverse transcriptase activity, and optionally in the absence of homologous recombination activity.50. Any above-numbered system, wherein the template RNA has been treated to reduce secondary structure, e.g., was heated, e.g., to a temperature that reduces secondary structure, e.g., to at least 70, 75, 80, 85, 90, or 95 C.51. The system of embodiment 50, wherein the template RNA was subsequently cooled, e.g., to a temperature that allows for secondary structure, e.g, to less than or equal to 30, 25, or 20 C52. A system for modifying DNA comprising:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide, (ii) a heterologous object sequence, (iii) a first homology domain having at least 10 bases of 100% identity to a target DNA strand, at the 5′ end of the template RNA, and (iv) a second homology domain having at least 10 bases of 100% identity to a target DNA strand, 5′ end of the template RNA.53. The system of any of the preceding embodiments, wherein (a) and (b) are part of the same nucleic acid.54. The system of any of embodiments 1-52, wherein (a) and (b) are separate nucleic acids.55. The system of any of the preceding embodiments, wherein the template RNA comprises at least 10 bases of 100% identity to a target DNA strand (e.g., wherein the target DNA strand is a human DNA sequence), at the 5′ end of the template RNA.56. The system of any of the preceding embodiments, wherein the template RNA comprises at least 10 bases of 100% identity to a target DNA strand (e.g., wherein the target DNA strand is a human DNA sequence), at the 3′ end of the template RNA.57. A host cell (e.g., a mammalian cell, e.g., a human cell) comprising any preceding numbered system.58. A method of modifying a target DNA strand in a cell, tissue or subject, comprising administering any preceding numbered system to the cell, tissue or subject, wherein the system reverse transcribes the template RNA sequence into the target DNA strand, thereby modifying the target DNA strand.59. The method of embodiment 58, wherein the cell, tissue or subject is a mammalian (e.g., human) cell, tissue or subject.60. The method of any of the preceding embodiments, wherein the cell is a fibroblast.61. The method of any of the preceding embodiments, wherein the cell is a primary cell.62. The method of any of the preceeding embodiments, where in the cell is not immortalized.63. A method of modifying the genome of a mammalian cell, comprising contacting the cell with:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain, (ii) an endonuclease domain, and optionally (iii) a DNA-binding domain; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.64. The method of embodiment 63, wherein the polypeptide does not comprise a target DNA binding domain.65. The method of embodiment 63, wherein the polypeptide is derived from an APE-type transposon reverse transcriptase.66. The method of embodiment 63, wherein the (i) a reverse transcriptase domain (ii) an endonuclease domain, or both of (i) and (ii), have a sequence of Table 1 or a sequence having at least 80%, 85%, 90%, 95%, 97%, 98%, 99%, 100% identity thereto.67. The method of embodiment 63, wherein the polypeptide further comprises a target DNA binding domain.68. A method of modifying the genome of a mammalian cell, comprising contacting the cell with:
  • (a) an RNA encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain, (ii) an endonuclease domain, and optionally (iii) a DNA-binding domain; and
  • (b) a template RNA comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence,
  • wherein the method does not comprise contacting the mammalian cell with DNA, or wherein the compositions of (a) and (b) do not comprise more than 1%, 0.5%, 0.2%, 0.1%, 0.05%, 0.02%, or 0.01% DNA by mass or by molar amount of nucleic acid.69. The method of embodiment 68, which results in the addition of at least 5, 10, 20, 50, 100, 200, 500, 1,000, 2,000, or 5,000 base pairs of exogenous DNA sequence to the genome of the mammalian cell.70. The method of embodiment 68 or 69, which results in the addition of a protein coding sequence to the genome of the mammalian cell.71. A method of inserting DNA into the genome of a mammalian cell, comprising contacting the cell with an RNA composition, wherein the RNA composition comprises:
  • (a) a first RNA that directs insertion of a template RNA into the genome, and
  • (b) a template RNA comprising a heterologous sequence,
  • wherein the method does not comprise contacting the mammalian cell with DNA, or wherein the compositions of (a) and (b) do not comprise more than 1%, 0.5%, 0.2%, 0.1%, 0.05%, 0.02%, or 0.01% DNA by mass or by molar amount of nucleic acid,
  • wherein the method results in the addition of at least 5, 10, 20, 50, 100, 200, 500, 1,000, 2,000, or 5,000 base pairs of DNA (e.g., exogenous DNA) sequence to the genome of the mammalian cell.72. The method of embodiment 71, wherein the first RNA encodes a polypeptide (e.g., a polypeptide of any of Tables 1, 2, or 3 herein), wherein the polypeptide directs insertion of the template RNA into the genome.73. The method of embodiments 72, wherein the template RNA further comprises a sequence that binds the polypeptide.74. A method of adding at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 500, 1000 bp of exogenous DNA to the genome of a mammalian cell, without delivery of DNA to the cell.75. A method of adding at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 500, 1000 bp of exogenous DNA to the genome of a mammalian cell, wherein the method does not comprise contacting the mammalian cell with DNA, or wherein the method comprises contacting the mammalian cell with a composition comprising less than 1%, 0.5%, 0.2%, 0.1%, 0.05%, 0.02%, or 0.01% DNA by mass or by molar amount of nucleic acid.76. A method of adding at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 500, 1000 bp of exogenous DNA to the genome of a mammalian cell, comprising delivering only RNA to the mammalian cell.77. A method of adding at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 500, 1000 bp of exogenous DNA to the genome of a mammalian cell, comprising delivering RNA and protein to the mammalian cell.78. The method of any one of embodiments 68-77, wherein the template RNA serves as the template for insertion of the exogenous DNA.79. The method of any one of embodiments 68-78, which does not comprise DNA-dependent RNA polymerization of exogenous DNA.80. The method of any of embodiments 58-79, which results in the addition of at least 5, 10, 20, 50, 100, 200, 500, 1,000, 2,000, or 5,000 base pairs of DNA to the genome of the mammalian cell.81. The methods of any of embodiments 68-80, wherein the RNA of (a) and the RNA of (b) are covalently linked, e.g., are part of the same transcript.82. The methods of any of embodiments 68-80, wherein the RNA of (a) and the RNA of (b) are separate RNAs.83. The method of any of embodiments 58-82, which does not comprise contacting the mammalian cell with a template DNA.84. A method of modifying the genome of a human cell, comprising contacting the cell with:
  • (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain, (ii) an endonuclease domain, and optionally (iii) a DNA-binding domain; and
  • (b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence,
  • wherein the method results in insertion of the heterologous object sequence into the human cell's genome,
  • wherein the human cell does not show upregulation of any DNA repair genes and/or tumor suppressor genes, or wherein no DNA repair gene and/or tumor suppressor gene is upregulated by more than 10%, 5%, 2%, or 1%, e.g., wherein upregulation is measured by RNA-seq, e.g., as described in Example 14.85. A method of adding an exogenous coding region to the genome of a cell (e.g., a mammalian cell), comprising contacting the cell with an RNA comprising the non-coding strand of the exogenous coding region, wherein optionally the RNA does not comprsise a coding strand of the exogenous coding region, wherein optionally the delivery comprises non-viral delivery.86. A method of expressing a polypeptide in a cell (e.g., a mammalian cell), comprising comprising contacting the cell with an RNA, wherein the RNA comprises a non-coding strand that is the reverse complement of a sequence that would encoding the polypeptide, wherein optionally the RNA does not comprsise a coding strand encoding the polypeptide, wherein optionally the delivery comprises non-viral delivery.87. The method of any of embodiments 58-86, wherein the sequence that is inserted into the mammalian genome is a sequence that is exogenous to the mammalian genome.88. The method of any of embodiments 58-87, which operates independently of a DNA template.89. The method of any of embodiments 58-88, wherein the cell is part of a tissue.90. The method of any of embodiments 58-89, wherein the mammalian cell is euploid, is not immortalized, is part of an organism, is a primary cell, is non-dividing, is a hepatocyte, or is from a subject having a genetic disease.91. The method of any of embodiments 58-90, wherein the contacting comprises contacting the cell with a plasmid, virus, viral-like particle, virosome, liposome, vesicle, exosome, or lipid nanoparticle.92. The method of any of embodiments 58-91, wherein the contacting comprises using non-viral delivery.93. The method of any of embodiments 58-92, which comprises comprising contacting the cell with the template RNA (or DNA encoding the template RNA), wherein the template RNA comprises the non-coding strand of an exogenous coding region, wherein optionally the template RNA does not comprise a coding strand of the exogenous coding region, wherein optionally the delivery comprises non-viral delivery, thereby adding the exogenous coding region to the genome of the cell.94. The method of any of embodiments 58-93, which comprises contacting the cell with the template RNA (or DNA encoding the template RNA), wherein the template RNA comprises a non-coding strand that is the reverse complement of a sequence that would encoding the polypeptide, wherein optionally the template RNA does not comprsise a coding strand encoding the polypeptide, wherein optionally the delivery comprises non-viral delivery, thereby expressing the polypeptide in the cell.95. The method of any of embodiments 63-94, wherein the contacting comprises administering (a) and (b) to a subject, e.g., intravenously.96. The method of any of embodiments 63-95, wherein the contacting comprises administering a dose of (a) and (b) to a subject at least twice.97. The method of any of embodiments 63-96, wherein the polypeptide reverse transcribes the template RNA sequence into the target DNA strand, thereby modifying the target DNA strand.98. The method of any embodiments 63-97, wherein (a) and (b) are administered separately.99. The method of any of embodiments 63-97, wherein (a) and (b) are administered together.100. The method of any of embodiments 63-99, wherein the nucleic acid of (a) is not integrated into the genome of the host cell.101. Any preceding numbered method, wherein the sequence that binds the polypeptide has one or more of the following characteristics:
  • (a) is at the 3′ end of the template RNA;
  • (b) is at the 5′ end of the template RNA;
  • (b) is a non-coding sequence;
  • (c) is a structured RNA; or
  • (d) forms at least 1 hairpin loop structures.102. Any preceding numbered method, wherein the template RNA further comprises a sequence comprising at least 20 nucleotides of at least 80% identity (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identity) to a target DNA strand.103. Any preceding numbered method, wherein the template RNA further comprises a sequence comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150 nucleotides of at least 80% identity (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identity) to a target DNA strand.104. Any preceding numbered method, wherein the sequence comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150 nucleotides, or about: 2-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 10-100, or 2-100 nucleotides, of at least 80% identity to a target DNA strand is at the 3′ end of the template RNA.105. Any preceding numbered method, wherein the template RNA further comprises a sequence comprising at least 100 nucleotides of at least 80% identity (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identity) to a target DNA strand, e.g., at the 3′ end of the template RNA.106. The method of embodiment 104 or 105, wherein the site in the target DNA strand to which the sequence comprises at least 80% identity is proximal to (e.g., within about: 0-10, 10-20, 20-30, 30-50, or 50-100 nucleotides of) a target site on the target DNA strand that is recognized (e.g., bound and/or cleaved) by the polypeptide comprising the endonuclease.107. Any preceding numbered method, wherein the sequence comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150 nucleotides, or about: 2-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 10-100, or 2-100 nucleotides, of at least 80% identity to a target DNA strand is at the 3′ end of the template RNA;
  • optionally wherein the site in the target DNA strand to which the sequence comprises at least 80% identity is proximal to (e.g., within about: 0-10, 10-20, or 20-30 nucleotides of) a target site on the target DNA strand that is recognized (e.g., bound and/or cleaved) by the polypeptide comprising the endonuclease.108. The method of embodiment 107, wherein the target site is the site in the human genome that has the closest identity to a native target site of the polypeptide comprising the endonuclease, e.g., wherein the target site in the human genome has at least about: 16, 17, 18, 19, or 20 nucleotides identical to the native target site.109. Any preceding numbered method, wherein the template RNA has at least 3, 4, 5, 6, 7, 8, 9, or 10 bases of 100% identity to the target DNA strand.110. Any preceding numbered method, wherein the at least 3, 4, 5, 6, 7, 8, 9, or 10 bases of 100% identity to the target DNA strand are at the 3′ end of the template RNA.111. Any preceding numbered method, wherein the at least 3, 4, 5, 6, 7, 8, 9, or 10 bases of 100% identity to the target DNA strand are at the 5′ end of the template RNA.112. Any preceding numbered method, wherein the template RNA comprises at least 3, 4, 5, 6, 7, 8, 9, or 10 bases of 100% identity to the target DNA strand at the 5′ end of the template RNA and at least 3, 4, 5, 6, 7, 8, 9, or 10 bases of 100% identity to the target DNA strand at the 3′ end of the template RNA.113. Any preceding numbered method, wherein the heterologous object sequence is between 50-50,000 base pairs (e.g., between 50-40,000 bp, between 500-30,000 bp between 500-20,000 bp, between 100-15,000 bp, between 500-10,000 bp, between 50-10,000 bp, between 50-5,000 bp).114. Any preceding numbered method, wherein the heterologous object sequence is at least 10, 25, 50, 100, 150, 200, 250, 300, 400, 500, 600, or 700 bp.115. Any preceding numbered method, wherein the heterologous object sequence is at least 715, 750, 800, 950, 1,000, 2,000, 3,000, or 4,000 bp.116. Any preceding numbered method, wherein the heterologous object sequence is less than 5,000, 10,000, 15,000, 20,000, 30,000, or 40,000 bp.117. Any preceding numbered method, wherein the heterologous object sequence is less than 700, 600, 500, 400, 300, 200, 150, or 100 bp.118. Any preceding numbered method, wherein the heterologous object sequence comprises:
  • (a) an open reading frame, e.g., a sequence encoding a polypeptide, e.g., an enzyme (e.g., a lysosomal enzyme), a membrane protein, a blood factor, an exon, an intracellular protein (e.g., a cytoplasmic protein, a nuclear protein, an organellar protein such as a mitochondrial protein or lysosomal protein), an extracellular protein, a structural protein, a signaling protein, a regulatory protein, a transport protein, a sensory protein, a motor protein, a defense protein, or a storage protein;
  • (b) a non-coding and/or regulatory sequence, e.g., a sequence that binds a transcriptional modulator, e.g., a promoter, an enhancer, an insulator;
  • (c) a splice acceptor site;
  • (d) a polyA site;
  • (e) an epigenetic modification site; or
  • (f) a gene expression unit.119. Any preceding numbered method, wherein the target DNA is a genomic safe harbor (GSH) site.120. Any preceding numbered method, wherein the target DNA is a genomic NATURAL HARBOR™ site.121. Any preceding numbered method, which results in insertion of the heterologous object sequence into the a target site in the genome at an average copy number of at least 0.01, 0.025, 0.05, 0.075, 0.1, 0.15, 0.2, 0.25, 0.3, 0.4, 0.5, 0.75, 1, 1.25, 1.5, 1.75, 2, 2.5, 3, 4, or 5 copies per genome.122. Any preceding numbered method, which results in about 25-100%, 50-100%, 60-100%, 70-100%, 75-95%, 80%-90%, of integrants into a target site in the genome being non-truncated, as measured by an assay described herein, e.g., an assay of Example 6.123. Any preceding numbered method, which results in insertion of the heterologous object sequence only at one target site in the genome of the cell.124. Any preceding numbered method, which results in insertion of the heterologous object sequence into a target site in a cell, wherein the insertered heterologous sequence comprises less than 10%, 5%, 2%, 1%, 0.5%, 0.2%, or 0.1% mutations (e.g., SNPs or one or more deletions, e.g., truncations or internal deletions) relative to the heterologous sequence prior to insertion, e.g., as measured by an assay of Example 12.125. Any preceding numbered method, which results in insertion of the heterologous object sequence into a target site in a plurality of cells, wherein less than 10%, 5%, 2%, or 1% of copies of the inserted heterologous sequence comprise a mutation (e.g., a SNP or a deletion, e.g., a truncation or an internal deletion), e.g., as measured by an assay of Example 12.126. Any preceding numbered method, which results in insertion of the heterologous object sequence into a target cell genome, and wherein the target cell does not show upregulation of p53, or shows upregulation of p53 by less than 10%, 5%, 2%, or 1%, e.g., wherein upregulation of p53 is measured by p53 protein level, e.g., according to the method described in Example 30, or by the level of p53 phosphorylated at Ser15 and Ser20.127. Any preceding numbered method, which results in insertion of the heterologous object sequence into a target cell genome, and wherein the target cell does not show upregulation of any DNA repair genes and/or tumor suppressor genes, or wherein no DNA repair gene and/or tumor suppressor gene is upregulated by more than 10%, 5%, 2%, or 1%, e.g., wherein upregulation is measured by RNA-seq, e.g., as described in Example 14.128. Any preceding numbered method, which results in insertion of the heterologous object sequence into the target site (e.g., at a copy number of 1 insertion or more than one insertion) in about 1-80% of cells in a population of cells contacted with the system, e.g., about: 1-10%, 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, or 70-80% of cells, e.g., as measured using single cell ddPCR, e.g., as described in Example 17.129. Any preceding numbered method, which results in insertion of the heterologous object sequence into the target site at a copy number of 1 insertion in about 1-80% of cells in a population of cells contacted with the system, e.g., about: 1-10%, 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, or 70-80% of cells, e.g., as measured using colony isolation and ddPCR, e.g., as described in Example 18.130. Any preceding numbered method, which results in insertion of the heterologous object sequence into the target site (on-target insertions) at a higher rate that insertion into a non-target site (off-target insertions) in a population of cells, wherein the ratio of on-target insertions to off-target insertions is greater than 10:1, 20:1, 30:1, 40:1, 50:1, 60:1, 70:1, 80:1. 90:1, 100:1, 200:1, 500:1, or 1,000:1, e.g., using an assay of Example 11.131. Any above-numbered method, results in insertion of a heterologous object sequence in the presence of an inhibitor of a DNA repair pathway (e.g., SCR7, a PARP inhibitor), or in a cell line deficient for a DNA repair pathway (e.g., a cell line deficient for the nucleotide excision repair pathway or the homology-directed repair pathway).132. Any preceding numbered system, formulated as a pharmaceutical composition.133. Any preceding numbered system, disposed in a pharmaceutically acceptable carrier (e.g., a vesicle, a liposome, a natural or synthetic lipid bilayer, a lipid nanoparticle, an exosome).134. A method of making a system for modifying the genome of a mammalian cell, comprising:
  • a) providing a template RNA as described in any of the preceding embodiments, e.g., wherein the template RNA comprises (i) a sequence that binds a polypeptide comprising a reverse transcriptase domain and an endonuclease domain, and (ii) a heterologous object sequence; and
  • b) treating the template RNA to reduce secondary structure, e.g., heating the template RNA, e.g., to at least 70, 75, 80, 85, 90, or 95 C, and
  • c) subsequently cooling the template RNA, e.g., to a temperature that allows for secondary structure, e.g, to less than or equal to 30, 25, or 20 C.135. The method of embodiment 134, which further comprises contacting the template RNA with a polypeptide that comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain, or with a nucleic acid (e.g., RNA) encoding the polypeptide.136. The method of embodiment 134 or 135, which further comprises contacting the template RNA with a cell.137. The system or method of any of the preceding embodiments, wherein the heterologous object sequence encodes a therapeutic polypeptide.138. The system or method of any of the preceding embodiments, wherein the heterologous object sequence encodes a mammalian (e.g., human) polypeptide, or a fragment or variant thereof.139. The system or method of any of the preceding embodiments, wherein the heterologous object sequence encodes an enzyme (e.g., a lysosomal enzyme), a blood factor (e.g., Factor I, II, V, VII, X, XI, XII or XIII), a membrane protein, an exon, an intracellular protein (e.g., a cytoplasmic protein, a nuclear protein, an organellar protein such as a mitochondrial protein or lysosomal protein), an extracellular protein, a structural protein, a signaling protein, a regulatory protein, a transport protein, a sensory protein, a motor protein, a defense protein, or a storage protein.140. The system or method of any of the preceding embodiments, wherein the heterologous object sequence comprises a tissue specific promoter or enhancer.141. The system or method of any of the preceding embodiments, wherein the heterologous object sequence encodes a polypeptide of greater than 250, 300, 400, 500, or 1,000 amino acids, and optionally up to 1300 amino acids.142. The system or method of any of the preceding embodiments, wherein the heterologous object sequence encodes a fragment of a mammalian gene but does not encode the full mammalian gene, e.g., encodes one or more exons but does not encode a full-length protein.143. The system or method of any of the preceding embodiments, wherein the heterologous object sequence encodes one or more introns.144. The system or method of any of the preceding embodiments, wherein the heterologous object sequence is other than a GFP, e.g., is other than a fluorescent protein or is other than a reporter protein.145. The system or method of any of the preceding embodiments, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain, wherein one or both of (i) or (ii) are derived from an avian retrotransposase, e.g., have a sequence of Table 2 or 3 or at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.146. The system or method of any of the preceding embodiments, wherein the polypeptide has an activity at 37° C. that is no less than 70%, 75%, 80%, 85%, 90%, or 95% of its activity at 25° C. under otherwise similar conditions.147. The system or method of any of the preceding embodiments, wherein the nucleic acid encoding the polypeptide and the template RNA or a nucleic acid encoding the template RNA are separate nucleic acids.148. The system or method of any of the preceding embodiments, wherein the template RNA does not encode an active reverse transcriptase, e.g., comprises an inactivated mutant reverse transcriptase, e.g., as described in Example 1 or 2, or does not comprise a reverse transcriptase sequence.149. The system or method of any of the preceding embodiments, wherein the template RNA comprises one or more chemical modifications.150. The system or method of any of the preceding embodiments, wherein the heterologous object sequence is disposed between the promoter and the sequence that binds the polypeptide.151. The system or method of any of the preceding embodiments, wherein the promoter is disposed between the heterologous object sequence and the sequence that binds the polypeptide.152. The system or method of any of the preceding embodiments, wherein the heterologous object sequence comprises an open reading frame (or the reverse complement thereof) in a 5′ to 3′ orientation on the template RNA.153. The system or method of any of the preceding embodiments, wherein the heterologous object sequence comprises an open reading frame (or the reverse complement thereof) in a 3′ to 5′ orientation on the template RNA.154. The system or method of any of the preceding embodiments, wherein the polypeptide comprises (a) a reverse transcriptase domain and (b) an endonuclease domain, wherein at least one of (a) or (b) is heterologous.155. The system or method of any of the preceding embodiments, wherein the polypeptide comprises (a) a target DNA binding domain, (b) a reverse transcriptase domain and (c) an endonuclease domain, wherein at least one of (a), (b) or (c) is heterologous.156. A substantially pure polypeptide comprising (a) a reverse transcriptase domain and (b) a heterologous endonuclease domain.157. A substantially pure polypeptide comprising (a) a target DNA binding domain, (b) a reverse transcriptase domain and (c) an endonuclease domain, wherein at least one of (a), (b) or (c) is heterologous.158. A substantially pure polypeptide comprising (a) a reverse transcriptase domain, (b) an endonuclease domain, and (c) a heterologous target DNA binding domain.159. A polypeptide or a nucleic acid encoding the polypeptide, wherein the polypeptide comprises (a) a reverse transcriptase domain and (b) an endonuclease domain, wherein at least one of (a) or (b) is heterologous to the other.160. A polypeptide or a nucleic acid encoding the polypeptide, wherein the polypeptide comprises (a) a target DNA binding domain, (b) a reverse transcriptase domain and (c) an endonuclease domain, wherein at least one of (a), (b) or (c) is heterologous to the other.161. Any polypeptide of numbered embodiments 156-160, wherein the reverse transcriptase domain has at least 80% identity (e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identity) to a reverse transcriptase domain of an APE-type or RLE-type non-LTR retrotransposon listed in any of Tables 1-3.162. Any polypeptide of numbered embodiments 156-161, wherein the endonuclease domain has at least 80% identity e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identity, to a endonuclease domain of an APE-type or RLE-type non-LTR retrotransposon listed in any of Tables 1-3.163. Any polypeptide of numbered embodiments 156-162 or any preceding numbered method, wherein the DNA binding domain has at least 80% identity e.g., at least 85%, 90%, 95%, 97%, 98%, 99%, 100% identity, to a DNA binding domain of a sequence listed in Table 1, 2, or 3.164. A nucleic acid encoding the polypeptide of any preceding numbered embodiment.165. A vector comprising the nucleic acid of numbered embodiment 164.166. A host cell comprising the nucleic acid of numbered embodiment 164.167. A host cell comprising the polypeptide of any preceding numbered embodiment.168. A host cell comprising the vector of numbered embodiment 165.169. A host cell (e.g., a human cell) comprising: (i) a heterologous object sequence (e.g., a sequence encoding a therapeutic polypeptide) at a target site in a chromosome, and (ii) one or both of an untranslated region (e.g., a retrotransposon untranslated sequence, e.g., a sequence of column 6 of Table 3) on one side (e.g., upstream) of the heterologous object sequence, and an untranslated region (e.g., a retrotransposon untranslated sequence, e.g., a sequence of column 7 of Table 3) on the other side (e.g., downstream) of the heterologous object sequence.170. A host cell (e.g., a human cell) comprising: (i) a heterologous object sequence (e.g., a sequence encoding a therapeutic polypeptide) at a target site in a chromosome, wherein the target locus is a NATURAL HARBOR™ site, e.g., a site of Table 4 herein.171. The host cell of embodiment 170, which further comprises (ii) one or both of an untranslated region 5′ of the heterologous object sequence, and an untranslated region 3′ of the heterologous object sequence.172. The host cell of embodiment 170, which further comprises (ii) one or both of an untranslated region (e.g., a retrotransposon untranslated sequence, e.g., a sequence of column 6 of Table 3) on one side (e.g., upstream) of the heterologous object sequence, and an untranslated region (e.g., a retrotransposon untranslated sequence, e.g., a sequence of column 7 of Table 3) on the other side (e.g., downstream) of the heterologous object sequence.173. The host cell of any of embodiments 169-173, which comprises heterologous object sequence at only the target site.174. A pharmaceutical composition, comprising any preceding numbered system, nucleic acid, polypeptide, or vector; and a pharmaceutically acceptable excipient or carrier.175. The pharmaceutical composition of embodiment 174, wherein the pharmaceutically acceptable excipient or carrier is selected from a vector (e.g., a viral or plasmid vector), a vesicle (e.g., a liposome, an exosome, a natural or synthetic lipid bilayer), a lipid nanoparticle.176. A polypeptide of any of the preceding embodiments, wherein the polypeptide further comprises a nuclear localization sequence.177. A method of modifying a target DNA strand in a cell, tissue or subject, comprising administering any preceding numbered system to the cell, tissue or subject, thereby modifying the target DNA strand.178. Any preceding numbered embodiment, wherein the polypeptide comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to an amino acid sequence listed in Table 5 (e.g., any one of SEQ ID NOs: 1017-1022), or a functional fragment thereof.179. Any preceding numbered embodiment, wherein the reverse transcriptase domain comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the reverse transcriptase domain of an amino acid sequence listed in Table 5 (e.g., any one of SEQ ID NOs: 1017-1022), or a functional fragment thereof.180. Any preceding numbered embodiment, wherein the retrotransposase comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to an amino acid sequence listed in Table 5 (e.g., any one of SEQ ID NOs: 1017-1022), or a functional fragment thereof.181. Any preceding numbered embodiment, wherein the polypeptide comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 1023) or GGGS (SEQ ID NO: 1024).182. Any preceding numbered embodiment, wherein the reverse transcriptase domain comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 1023) or GGGS (SEQ ID NO: 1024).183. Any preceding numbered embodiment, wherein the retrotransposase comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 1023) or GGGS (SEQ ID NO: 1024).184. Any preceding numbered embodiment, wherein the polypeptide, reverse transcriptase domain, or retrotransposase comprises a linker comprising an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 1023) or GGGS (SEQ ID NO: 1024).185. Any preceding numbered embodiment, wherein the polypeptide comprises a DNA binding doman covalently attached to the remainder of the polypeptide by a linker, e.g., a linker comprising at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 125, 150, 200, 300, 400, or 500 amino acids.186. Numbered embodiment 185, wherein the linker is attached to the remainder of the polypeptide at a position in the DNA binding domain, RNA binding domain, reverse transcriptase domain, or endonuclease domain (e.g., as shown in any of FIGS. 17A-17F).187. Numbered embodiment 185 or 186, wherein the linker is attached to the remainder of the polypeptide at a position in the N-terminal side of an alpha helical region of the polypeptide, e.g., at a position corresponding to version v1 as described in Example 26.188. Numbered embodiment 185 or 186, wherein the linker is attached to the remainder of the polypeptide at a position in the C-terminal side of an alpha helical region of the polypeptide, e.g., preceding an RNA binding motif (e.g., a −1 RNA binding motif), e.g., at a position corresponding to version v2 as described in Example 26.189. Numbered embodiment 185 or 186, wherein the linker is attached to the remainder of the polypeptide at a position in the C-terminal side of a random coil region of the polypeptide, e.g., N-terminal relative to a DNA binding motif (e.g., a c-myb DNA binding motif), e.g., at a position corresponding to version v3 as described in Example 26.190. Any one of numbered embodiments 185-189, wherein the linker comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 1023) or GGGS (SEQ ID NO: 1024).191. Any preceding numbered embodiment, wherein a polynucleotide sequence comprising at least about 500, 1000, 2000, 3000, 3500, 3600, 3700, 3800, 3900, or 4000 contiguous nucleotides from the 5′ end of the template RNA sequence are integrated into a target cell genome.192. Any preceding numbered embodiment, wherein a polynucleotide sequence comprising at least about 500, 1000, 2000, 2500, 2600, 2700, 2800, 2900, or 3000 contiguous nucleotides from the 3′ end of the template RNA sequence are integrated into a target cell genome.193. Any preceding numbered embodiment, wherein the nucleic acid sequence of the template RNA, or a portion thereof (e.g., a portion comprising at least about 100, 200, 300, 400, 500, 1000, 2000, 2500, 3000, 3500, or 4000 nucleotides) integrates into the genomes of a population of target cells at a copy number of at least about 0.21, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or 1.0 integrants/genome.194. Any preceding numbered embodiment, wherein the nucleic acid sequence of the template RNA, or a portion thereof (e.g., a portion comprising at least about 100, 200, 300, 400, 500, 1000, 2000, 2500, 3000, 3500, or 4000 nucleotides) integrates into the genomes of a population of target cells at a copy number of at least about 0.085, 0.09, 0.1, 0.15, or 0.2 integrants/genome.195. Any preceding numbered embodiment, wherein the nucleic acid sequence of the template RNA, or a portion thereof (e.g., a portion comprising at least about 100, 200, 300, 400, 500, 1000, 2000, 2500, 3000, 3500, or 4000 nucleotides) integrates into the genomes of a population of target cells at a copy number of at least about 0.036, 0.04, 0.05, 0.06, 0.07, or 0.08 integrants/genome.196. Any preceding numbered embodiment, wherein the polypeptide comprises a functional endonuclease domain (e.g., wherein the endonuclease domain does not comprise a mutation that abolishes endonuclease activity, e.g., as described herein).197. Any preceding numbered embodiment, wherein the polypeptide comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the R2 polypeptide from a medium ground finch, e.g., Geospiza fortis (e.g., as described herein, e.g., R2-1_GFo), or a functional fragment thereof.198. Any preceding numbered embodiment, wherein the reverse transcriptase domain comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the R2 polypeptide from a medium ground finch, e.g., Geospiza fortis (e.g., as described herein, e.g., R2-1_GFo), or a functional fragment thereof.199. Any preceding numbered embodiment, wherein the retrotransposase comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the R2 polypeptide from a medium ground finch, e.g., Geospiza fortis (e.g., as described herein, e.g., R2-1_GFo), or a functional fragment thereof.200. Any one of numbered embodiments 197-199, wherein the nucleic acid sequence of the template RNA, or a portion thereof (e.g., a portion comprising at least about 100, 200, 300, 400, 500, 1000, 2000, 2500, 3000, 3500, or 4000 nucleotides) integrates into the genomes of a population of target cells at a copy number of at least about 0.21 integrants/genome.201. Any preceding numbered embodiment, wherein the polypeptide comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the R4 polypeptidefrom a large roundworm, e.g., Ascaris lumbricoides (e.g., as described herein, e.g., R4_AL), or a functional fragment thereof.202. Any preceding numbered embodiment, wherein the reverse transcriptase domain comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the R4 polypeptidefrom a large roundworm, e.g., Ascaris lumbricoides (e.g., as described herein, e.g., R4_AL), or a functional fragment thereof.203. Any preceding numbered embodiment, wherein the retrotransposase comprises an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the R4 polypeptidefrom a large roundworm, e.g., Ascaris lumbricoides (e.g., as described herein, e.g., R4_AL), or a functional fragment thereof.204. Any one of numbered embodiments 201-203, wherein the nucleic acid sequence of the template RNA, or a portion thereof (e.g., a portion comprising at least about 100, 200, 300, 400, 500, 1000, 2000, 2500, 3000, 3500, or 4000 nucleotides) integrates into the genomes of a population of target cells at a copy number of at least about 0.085 integrants/genome.205. Any preceding numbered embodiment, wherein introduction of the system into a target cell does not result in alteration (e.g., upregulation) of p53 and/or p21 protein levels, H2AX phosphorylation (e.g., gamma H2AX), ATM phosphorylation, ATR phosphorylation, Chk1 phosphorylation, Chk2 phosphorylation, and/or p53 phosphorylation.206. Any preceding numbered embodiment, wherein introduction of the system into a target cell results in upregulation of p53 protein level in the target cell to a level that is less than about 0.001%, 0.005%, 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 30%, 40%, 45%, 50%, 55%, 60%, 70%, 80%, or 90% of the p53 protein level induced by introducing a site-specific nuclease, e.g., Cas9, that targets the same genomic site as said system.207. Numbered embodiment 205 or 206, wherein the p53 protein level is determined according to the method described in Example 30.208. Any preceding numbered embodiment, wherein introduction of the system into a target cell results in upregulation of p53 phosphorylation level in the target cell to a level that is less than about 0.001%, 0.005%, 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 30%, 40%, 45%, 50%, 55%, 60%, 70%, 80%, or 90% of the p53 phosphorylation level induced by introducing a site-specific nuclease, e.g., Cas9, that targets the same genomic site as said system.209. Any preceding numbered embodiment, wherein introduction of the system into a target cell results in upregulation of p21 protein level in the target cell to a level that is less than about 0.001%, 0.005%, 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 30%, 40%, 45%, 50%, 55%, 60%, 70%, 80%, or 90% of the p53 protein level induced by introducing a site-specific nuclease, e.g., Cas9, that targets the same genomic site as said system.210. Numbered embodiment 205 or 209, wherein the p21 protein level is determined according to the method described in Example 30.211. Any preceding numbered embodiment, wherein introduction of the system into a target cell results in upregulation of H2AX phosphorylation level in the target cell to a level that is less than about 0.001%, 0.005%, 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 30%, 40%, 45%, 50%, 55%, 60%, 70%, 80%, or 90% of the H2AX phosphorylation level induced by introducing a site-specific nuclease, e.g., Cas9, that targets the same genomic site as said system.212. Any preceding numbered embodiment, wherein introduction of the system into a target cell results in upregulation of ATM phosphorylation level in the target cell to a level that is less than about 0.001%, 0.005%, 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 30%, 40%, 45%, 50%, 55%, 60%, 70%, 80%, or 90% of the ATM phosphorylation level induced by introducing a site-specific nuclease, e.g., Cas9, that targets the same genomic site as said system.213. Any preceding numbered embodiment, wherein introduction of the system into a target cell results in upregulation of ATR phosphorylation level in the target cell to a level that is less than about 0.001%, 0.005%, 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 30%, 40%, 45%, 50%, 55%, 60%, 70%, 80%, or 90% of the ATR phosphorylation level induced by introducing a site-specific nuclease, e.g., Cas9, that targets the same genomic site as said system.214. Any preceding numbered embodiment, wherein introduction of the system into a target cell results in upregulation of Chk1 phosphorylation level in the target cell to a level that is less than about 0.001%, 0.005%, 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 30%, 40%, 45%, 50%, 55%, 60%, 70%, 80%, or 90% of the Chk1 phosphorylation level induced by introducing a site-specific nuclease, e.g., Cas9, that targets the same genomic site as said system.215. Any preceding numbered embodiment, wherein introduction of the system into a target cell results in upregulation of Chk2 phosphorylation level in the target cell to a level that is less than about 0.001%, 0.005%, 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 30%, 40%, 45%, 50%, 55%, 60%, 70%, 80%, or 90% of the Chk2 phosphorylation level induced by introducing a site-specific nuclease, e.g., Cas9, that targets the same genomic site as said system.

Definitions

Domain: The term “domain” as used herein refers to a structure of a biomolecule that contributes to a specified function of the biomolecule. A domain may comprise a contiguous region (e.g., a contiguous sequence) or distinct, non-contiguous regions (e.g., non-contiguous sequences) of a biomolecule. Examples of protein domains include, but are not limited to, an endonuclease domain, a DNA binding domain, a reverse transcription domain; an example of a domain of a nucleic acid is a regulatory domain, such as a transcription factor binding domain.

Exogenous: As used herein, the term exogenous, when used with reference to a biomolecule (such as a nucleic acid sequence or polypeptide) means that the biomolecule was introduced into a host genome, cell or organism by the hand of man. For example, a nucleic acid that is as added into an existing genome, cell, tissue or subject using recombinant DNA techniques or other methods is exogenous to the existing nucleic acid sequence, cell, tissue or subject.

Genomic safe harbor site (GSH site): A genomic safe harbor site is a site in a host genome that is able to accommodate the integration of new genetic material, e.g., such that the inserted genetic element does not cause significant alterations of the host genome posing a risk to the host cell or organism. A GSH site generally meets 1, 2, 3, 4, 5, 6, 7, 8 or 9 of the following criteria: (i) is located >300 kb from a cancer-related gene; (ii) is >300 kb from a miRNA/other functional small RNA; (iii) is >50 kb from a 5′ gene end; (iv) is >50 kb from a replication origin; (v) is >50 kb away from any ultraconservered element; (vi) has low transcriptional activity (i.e. no mRNA+/−25 kb); (vii) is not in copy number variable region; (viii) is in open chromatin; and/or (ix) is unique, with 1 copy in the human genome. Examples of GSH sites in the human genome that meet some or all of these criteria include (i) the adeno-associated virus site 1 (AAVS1), a naturally occurring site of integration of AAV virus on chromosome 19; (ii) the chemokine (C—C motif) receptor 5 (CCR5) gene, a chemokine receptor gene known as an HIV-1 coreceptor; (iii) the human ortholog of the mouse Rosa26 locus; (iv) the rDNA locus. Additional GSH sites are known and described, e.g., in Pellenz et al. epub Aug. 20, 2018 (doi.org/10.1101/396390).

Heterologous: The term heterologous, when used to describe a first element in reference to a second element means that the first element and second element do not exist in nature disposed as described. For example, a heterologous polypeptide, nucleic acid molecule, construct or sequence refers to (a) a polypeptide, nucleic acid molecule or portion of a polypeptide or nucleic acid molecule sequence that is not native to a cell in which it is expressed, (b) a polypeptide or nucleic acid molecule or portion of a polypeptide or nucleic acid molecule that has been altered or mutated relative to its native state, or (c) a polypeptide or nucleic acid molecule with an altered expression as compared to the native expression levels under similar conditions. For example, a heterologous regulatory sequence (e.g., promoter, enhancer) may be used to regulate expression of a gene or a nucleic acid molecule in a way that is different than the gene or a nucleic acid molecule is normally expressed in nature. In another example, a heterologous domain of a polypeptide or nucleic acid sequence (e.g., a DNA binding domain of a polypeptide or nucleic acid encoding a DNA binding domain of a polypeptide) may be disposed relative to other domains or may be a different sequence or from a different source, relative to other domains or portions of a polypeptide or its encoding nucleic acid. In certain embodiments, a heterologous nucleic acid molecule may exist in a native host cell genome, but may have an altered expression level or have a different sequence or both. In other embodiments, heterologous nucleic acid molecules may not be endogenous to a host cell or host genome but instead may have been introduced into a host cell by transformation (e.g., transfection, electroporation), wherein the added molecule may integrate into the host genome or can exist as extra-chromosomal genetic material either transiently (e.g., mRNA) or semi-stably for more than one generation (e.g., episomal viral vector, plasmid or other self-replicating vector).

Mutation or Mutated: The term “mutated” when applied to nucleic acid sequences means that nucleotides in a nucleic acid sequence may be inserted, deleted or changed compared to a reference (e.g., native) nucleic acid sequence. A single alteration may be made at a locus (a point mutation) or multiple nucleotides may be inserted, deleted or changed at a single locus. In addition, one or more alterations may be made at any number of loci within a nucleic acid sequence. A nucleic acid sequence may be mutated by any method known in the art.

Nucleic acid molecule: Nucleic acid molecule refers to both RNA and DNA molecules including, without limitation, cDNA, genomic DNA and mRNA, and also includes synthetic nucleic acid molecules, such as those that are chemically synthesized or recombinantly produced, such as RNA templates, as described herein. The nucleic acid molecule can be double-stranded or single-stranded, circular or linear. If single-stranded, the nucleic acid molecule can be the sense strand or the antisense strand. Unless otherwise indicated, and as an example for all sequences described herein under the general format “SEQ. ID NO:,” “nucleic acid comprising SEQ. ID NO:1” refers to a nucleic acid, at least a portion which has either (i) the sequence of SEQ. ID NO: 1, or (ii) a sequence complimentary to SEQ. ID NO:1. The choice between the two is dictated by the context in which SEQ. ID NO:1 is used. For instance, if the nucleic acid is used as a probe, the choice between the two is dictated by the requirement that the probe be complimentary to the desired target. Nucleic acid sequences of the present disclosure may be modified chemically or biochemically or may contain non-natural or derivatized nucleotide bases, as will be readily appreciated by those of skill in the art. Such modifications include, for example, labels, methylation, substitution of one or more naturally occurring nucleotides with an analog, inter-nucleotide modifications such as uncharged linkages (for example, methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, etc.), charged linkages (for example, phosphorothioates, phosphorodithioates, etc.), pendant moieties, (for example, polypeptides), intercalators (for example, acridine, psoralen, etc.), chelators, alkylators, and modified linkages (for example, alpha anomeric nucleic acids, etc.). Also included are synthetic molecules that mimic polynucleotides in their ability to bind to a designated sequence via hydrogen bonding and other chemical interactions. Such molecules are known in the art and include, for example, those in which peptide linkages substitute for phosphate linkages in the backbone of a molecule. Other modifications can include, for example, analogs in which the ribose ring contains a bridging moiety or other structure such as modifications found in “locked” nucleic acids.

Gene expression unit: a gene expression unit is a nucleic acid sequence comprising at least one regulatory nucleic acid sequence operably linked to at least one effector sequence. A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter or enhancer is operably linked to a coding sequence if the promoter or enhancer affects the transcription or expression of the coding sequence. Operably linked DNA sequences may be contiguous or non-contiguous. Where necessary to join two protein-coding regions, operably linked sequences may be in the same reading frame.

Host: The terms host genome or host cell, as used herein, refer to a cell and/or its genome into which protein and/or genetic material has been introduced. It should be understood that such terms are intended to refer not only to the particular subject cell and/or genome, but to the progeny of such a cell and/or the genome of the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein. A host genome or host cell may be an isolated cell or cell line grown in culture, or genomic material isolated from such a cell or cell line, or may be a host cell or host genome which composing living tissue or an organism. In some instances, a host cell may be an animal cell or a plant cell, e.g., as described herein. In certain instances, a host cell may be a bovine cell, horse cell, pig cell, goat cell, sheep cell, chicken cell, or turkey cell. In certain instances, a host cell may be a corn cell, soy cell, wheat cell, or rice cell.

Pseudoknot: A “pseudoknot sequence” sequence, as used herein, refers to a nucleic acid (e.g., RNA) having a sequence with suitable self-complementarity to form a pseudoknot structure, e.g., having: a first segment, a second segment between the first segment and a third segment, wherein the third segment is complementary to the first segment, and a fourth segment, wherein the fourth segment is complementary to the second segment. The pseudoknot may optionally have additional secondary structure, e.g., a stem loop disposed in the second segment, a stem-loop disposed between the second segment and third segment, sequence before the first segment, or sequence after the fourth segment. The pseudoknot may have additional sequence between the first and second segments, between the second and third segments, or between the third and fourth segments. In some embodiments, the segments are arranged, from 5′ to 3′: first, second, third, and fourth. In some embodiments, the first and third segments comprise five base pairs of perfect complementarity. In some embodiments, the second and fourth segments comprise 10 base pairs, optionally with one or more (e.g., two) bulges. In some embodiments, the second segment comprises one or more unpaired nucleotides, e.g., forming a loop. In some embodiments, the third segment comprises one or more unpaired nucleotides, e.g., forming a loop.

Stem-loop sequence: As used herein, a “stem-loop sequence” refers to a nucleic acid sequence (e.g., RNA sequence) with sufficient self-complementarity to form a stem-loop, e.g., having a stem comprising at least two (e.g., 3, 4, 5, 6, 7, 8, 9, or 10) base pairs, and a loop with at least three (e.g., four) base pairs. The stem may comprise mismatches or bulges.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic of the GENE WRITING™ genome editing system.

FIG. 2 is a schematic of the structure of the GENE WRITER™ genome editor polypeptide.

FIG. 3 is a schematic of a GENE WRITER™ genome editor polypeptide comprising a heterologous DNA binding domain designed to target different sites of the genome.

FIG. 4 is a schematic of the structure of GENE WRITER™ genome editor template RNA.

FIG. 5 is a schematic showing the GENE WRITING™ genome editing system to add a gene expression unit into a safe harbor site in the genome.

FIG. 6 is a schematic showing GENE WRITING™ genome editing to add a new exon into an specific intron in the genome and replace downstream exons.

FIG. 7 illustrates a schematic of MISEQ™ library construction. Nested PCR was performed across the R2Tg-rDNA junction using (1) outer forward primer and tailed inner reverse primer followed by (2) tailed inner forward primer and tail reverse primer. The inner reverse primer contains a 1-4 base stagger, an 8-nucleotide randomized UMI, and a multiplexing barcode. The UMI allows for counting of individual amplification events to eliminate PCR bias.

FIGS. 8A-8B: Results of MISEQ™ and MATLAB™ analysis of DNA-mediated R2Tg integration into Hek293T cells. Each graph shows analysis of (FIG. 8A) the experimental R2Tg (FIG. 8B) and 1 bp deletion negative control. The y-axis indicates aligned counts of unique sequences determined via unique UMIs found via MATLAB™. The X-axis indicates the sequence position of sequence coverage. The vertical gray line at the left of the graph indicates the position of the forward primer, while the vertical gray line at the right of the graph indicates the expected Tg-rDNA junction site. Bars at the right end of the graph indicate insertion without a truncation, and bars at the left end of the graph indicate truncation. FIG. 8A shows that most sequences show high alignment to the expected integration product.

FIG. 9 shows a ddPCR evaluation of copy number variation of the R2Tg-rDNA junction in human cells across transfection conditions. Forward primer and probe were expected to bind to the 3′ UTR of the R2Tg, while reverse primer was targeted to the human rDNA. The resulting ddPCR signal was normalized to that of reference assay RPP30 to determine copy number. Significantly higher average copies per genome were found with the wildtype (WT, left set of bars) R2Tg as compared to genetic control altering translation with a 1-bp deletion (Frameshift mutant control, right set of bars).

FIG. 10 illustrates the sequence alignment and coverage of TOPO cloning the nested PCR product from Example 7. The gray line at the right edge of the graph indicates the expected transgene-rDNA junction. Most sequences showed high alignment to the expected integrated product.

FIG. 11 is a schematic of an exemplary template RNA. It comprises a payload domain in the center (e.g., a heterologous object sequence, e.g., comprising a promoter and a protein-coding sequence). The payload domain is flanked by 5′ and 3′ protein interaction domains, e.g., sequences capable of binding the GENE WRITER™ polypeptide, e.g., 5′ and 3′ UTR sequences shown in Table 3. Flanking the protein interaction domains are 5′ and 3′ homology domains, which have homology to the desired insertion region in the genome.

FIG. 12 is a graph showing retrotransposition efficiency measured by ddPCR (digital droplet PCR) using different transfection conditions. Bars A-C represent samples that were transfected using 0.15μl Lipofectamine™ RNAiMAX with 100 ng, 250 ng, or 500 ng respectively. Bars D-F represent samples that were transfected using 0.3 μl Lipofectamine™ RNAiMAX with 100 ng, 250 ng, or 500 ng respectively. Bars G-I represent samples that were transfected using 1 μl TransIT®-mRNA transfection kit with 100 ng, 250 ng, or 500 ng respectively.

FIG. 13. Schematic of trans-transgene delivery machinery. This schematic illustrates a driver plasmid (left) with a pCEP4 backbone, which encodes the reverse transcriptase R2Tg, with a promoter and Kozak sequence upstream, and a polyadenylation signal downstream. The driver plasmid can drive expression of the GENE WRITER™ protein. The transgene plasmid (right), with a pCDNA backbone, comprises (in order) a CMV promoter, an rDNA homology sequence, a 5′ UTR, an antisense-orientation insert, a 3′ UTR, a second rDNA homology sequence, a second polyadenylation signal, and a TK promoter driving a mKate2 marker. The antisense-orientation insert comprises an EF1α promoter, a coding region for EGFP that comprises an intron, and a polyadenylation signal. Use of the CMV promoter in the trangene plasmid drives expression of a template RNA comprising the rDNA homology regions, the UTRs, and the antisense-orientation insert.

FIG. 14 shows ddPCR evaluation of copy number variation of the transgene-rDNA junction in human cells across transfection conditions. Forward primer and probe were designed to bind to the 3′ UTR of the R2Tg, while reverse primer was targeted to the human rDNA. The resulting ddPCR signal was normalized to that of reference assay RPP30 to determine copy number. Significantly higher average copies per genome were found with the wildtype (WT) R2Tg as compared to backbone construct with no R2Tg sequence involved. Condition 1 denotes a driver plasmid: transgene plasmid molar ratio of 9:1; condition 2 denotes the ratio is 4:1, condition 3 denotes the ratio is 1:1, condition 4 denotes the ratio is 1:4, and condition 5 denotes the ratio is 1:9.

FIGS. 15A and 15B. FIG. 15A: Hybrid capture of R2Tg identified on-target integrations in the human genome. The read coverage as aligned to the expected target integration in the R2 ribosomal site is indicated on the y-axis. The 5′ junction between rDNA and R2Tg is indicated by the left vertical line, while the 3′ junction is indicated by the right vertical line. Next-generation sequencing identifies reads spanning the expected junctions. FIG. 15B shows the number of reads from this experiment categorized as on-target integration or off-target integration at the 5′ end and 3′ end of the integrated sequence.

FIG. 16. Sanger sequencing result of the 3′ junction nested PCR. Lowercase nucleotides represent the designed SNP. Shaded uppercase nucleotides represent WT sequence. FIG. 16 discloses SEQ ID NO: 1538.

FIGS. 17A-17F are schematic diagrams depicting various covalently dimerized GENE WRITER™ protein configurations. The proteins depicted are. FIG. 17A. a wild-type full length enzyme. FIG. 17B, two full-length enzymes (each comprising a DNA-binding domain, an RNA-binding domain, a reverse transcriptase domain, and an endonuclease domain) connected by a linker. FIG. 17C, a DNA binding domain and an RNA binding domain connected by a linker to a full-length enzyme. FIG. 17D, a DNA-binding domain and an RNA-binding domain connected by a linker to an RNA-binding domain, a reverse transcriptase domain, and an endonuclease domain. FIG. 17E, a DNA-binding domain connected by a first linker to an RNA-binding domain, which is connected by a second linker to a second RNA-binding domain, a reverse transcriptase domain, and an endonuclease domain. FIG. 17F, a DNA-binding domain connected by a first linker to an RNA-binding domain, which is connected by a second linker to a plurality of RNA-binding domains (in this figure, the molecule comprises three RNA-binding domains), which are connected by a linker to a reverse transcriptase domain and an endonuclease domain. In some embodiments, each R2 binds UTRs in the template RNA. In some embodiments, at least one module comprises a reverse transcriptase domain and an endonuclease domain. In some embodiments, the protein comprises a plurality of RNA-binding domains. In some embodiments, the modular system is split and is only active when it binds on DNA where the system uses two different DNA binding modules, e.g., a first protein comprising a first DNA binding module that is fused to an RNA binding module that recruits the RNA template for target primed reverse transcription, and second protein that comprises a second DNA binding module that binds at the site of intergration and is fused to the reverse transcription and endonuclease modules. In some embodiments, the nucleic acid encoding the GENE WRITER™ comprises an intein such that the GENE WRITER™ protein is expressed from two separate genes and is fused by protein splicing after being translated. In some embodiments, the GENE WRITER™ is derived from a non-LTR protein, e.g., an R2 protein.

FIGS. 18A-18F are a schematic diagam showing different modular components of a GENE WRITER™ protein. The proteins depicted are: FIG. 18A: a wild-type full length enzyme. FIG. 18B: the DNA-binding domain of a GENE WRITER™ may comprise zinc fingers, Cas9, or a transcription factor, or a fragment or variant of any of the forgoing. FIG. 18C: the reverse transcriptase domain and RNA-binding domain together may comprise a reverse transcriptase domain (e.g., from an R2 protein) that is heterologous to one or more other domains of the protein, and may optionally futher comprise one or more additional RNA binding domains, or a fragment or variant of any of the foregoing. FIG. 18D: the RNA binding domain may comprise, e.g., a B-box protein, an MS2 coat protein, a dCas protein, or a UTR binding protein, or a fragment or variant of any of the foregoing. FIG. 18E: the reverse transcriptase domain may comprise, e.g., a truncated reverse transcriptase domain, e.g., from an R2 protein; a reverse transcriptase domain from a virus (e.g., HIV), or a reverse transcriptase domain from AMV (avian myeloblastosis virus), or a fragment or variant of any of the foregoing. FIG. 18F: the endonuclease domain can comprise, e.g., a Cas9 nickase, a Cas ortholog, Fok I, or a restriction enzyme, or a fragment or variant of any of the foregoing. In some embodiments, a separate DNA binding domain can be attached to a polypeptide described herein (e.g., a DNA binding domain having stronger affinity for the target DNA sequence than an existing or prior DNA binding domain of the polypeptide, or a DNA binding sequence that binds to a different target DNA sequence than the existing or prior DNA binding domain of the polypeptide). In some embodiments, DNA binding domain mutants can be generated, e.g., having increased affinity to the target DNA sequence. In embodiments, the DNA binding domain comprises a zinc finger. In embodiments, the DNA binding domain is attached to the polypeptide (e.g., at the N-terminal or C-terminal ends) via a linker, e.g., as described herein. In embodiments, a zinc finger is attached to a DNA binding domain mutant (e.g., as described herein), such that the polypeptide exhibits increased binding to the target DNA sequence (e.g., as dictated by the zinc finger) without competition with the rDNA.

FIG. 19 is a graph showing linker mutant integration into the genome of HEK293T cells, assessed by a ddPCR assay evaluating copy number of R2Tg integration per genome. In v1 mutants, an insertion is located at the N-terminal side of an alpha helical region of R2Tg that preceded the predicted −1 RNA binding motif, in v2 mutants, an insertion is located at the C-terminal side of an alpha helical region of R2Tg that preceded the predicted −1 RNA binding motif, and in v3 mutants, an insertion is located C-terminal to a random coil region that came after the predicted c-myb DNA binding motif of R2Tg.

FIGS. 20A-20B are a series of graphs showing long-read sequencing confirming fidelity of R2Tg cis integration. Unique sequence coverage, as determined by UMI, is graphed across the expected reference sequence. The left vertical bar indicates expected 5′ junction of the rDNA and R2Tg, while the right vertical bar indicates the 3′ junction. Two separate amplicons spanning the 5′ junction and 3′ junction are shown.

FIGS. 21A-21B are a series of graphs showing long-read sequencing confirming fidelity of R2Tg cis integration. Unique sequence deletions (>3 bp) as determined by UMI is graphed across the expected reference sequence. The left vertical bar indicates expected 5′ junction of the rDNA and R2Tg, while the right vertical bar indicates the 3′ junction. Two separate amplicons spanning the 5′ junction and 3′ junction are shown.

FIG. 22 is a diagram showing exemplary plasmid map PLV033 for cis integration of R2Gfo.

FIG. 23 is a graph showing integration of R2Gfo, R4Al, and R2Tg in cis in HEK293T cells. The mean of four replicates is shown; error bars indicate standard deviation.

FIG. 24 is a graph showing that R2Tg integrates into human fibroblasts in cis. Integration efficiency of the wild-type (WT) and endonuclease (EN) control R2Tg were plotted over four replicate experiments as measured via ddPCR at the 3′ junction of R2Tg and the rDNA target.

FIG. 25 is a diagram showing Western Blot analysis for p53, p21, Actin, and Vinculin. U2OS cells were trested with the indicated compound or plasmid: GFP, R2Tg-WT (wild-type), or R2Tg-EN (endonuclease domain mutant). Plasmid transfections were performed with either lipofectamine 3000 (Lipo) or Fugene HD (Fug). Cells were analyzed 24 hours after treatment or transfection.

DETAILED DESCRIPTION

This disclosure relates to compositions, systems and methods for targeting, editing, modifying or manipulating a DNA sequence (e.g., inserting a heterologous object DNA sequence into a target site of a mammalian genome) at one or more locations in a DNA sequence in a cell, tissue or subject, e.g., in vivo or in vitro. The object DNA sequence may include, e.g., a coding sequence, a regulatory sequence, a gene expression unit.

More specifically, the disclosure provides retrotransposon-based systems for inserting a sequence of interest into the genome. This disclosure is based, in part, on a bioinformatic analysis to identify retrotransposase sequences and the associated 5′ UTR and 3′ UTR from a variety of organisms (see Table 3). While not wishing to be bound by theory, in some embodiments, retrotransposases identified in homeothermic (warm blooded) species, like birds, may have improved thermostability relative to some other enzymes that evolved at lower temperatures, and the thermostable retrotransposases may therefore be better suited for use in human cells. The disclosure also provides experimental evidence that several retrotransposases from different species, e.g., different species of animal and/or different species and clade of retrotransposon (e.g., as grouped by reverse transcriptase phylogeny, e.g., as described in Su et al. (2019) RNA; incorporated herein by reference in its entirety), can be used to catalyze DNA insertion into a target site in human cells (see Examples 7 and Example 28).

In some embodiments, systems described herein can have a number of advantages relative to various earlier systems. For instance, the disclosure describes retrotransposases capable of inserting long sequences (e.g., over 3000 nucleotides) of heterologous nucleic acid into a genome (see, e.g., FIG. 20A). In addition, retrotransposases described herein can insert heterologous nucleic acid in an endogenous site in the genome, such as the rDNA locus (see, e.g., Example 7). This is in contrast to Cre/loxP systems which require a first step of inserting an exogenous loxP site before a second step of inserting a sequence of interest into the loxP site.

GENE WRITER™ Genome Editors

Non-long terminal repeat (LTR) retrotransposons are a type of mobile genetic elements that are widespread in eukaryotic genomes. They include two classes: the apurinic/apyrimidinic endonuclease (APE)-type and the restriction enzyme-like endonuclease (RLE)-type. The APE class retrotransposons are comprised of two functional domains: an endonuclease/DNA binding domain, and a reverse transcriptase domain. The RLE class are comprised of three functional domains: a DNA binding domain, a reverse transcription domain, and an endonuclease domain. The reverse transcriptase domain of non-LTR retrotransposon functions by binding an RNA sequence template and reverse transcribing it into the host genome's target DNA. The RNA sequence template has a 3′ untranslated region which is specifically bound to the transposase, and a variable 5′ region generally having Open Reading Frame(s) (“ORF”) encoding transposase proteins. The RNA sequence template may also comprise a 5′ untranslated region which specifically binds the retrotransposase.

The inventors have found that, surprisingly, the elements of such non-LTR retrotransposons can be functionally modularized and/or modified to target, edit, modify or manipulate a target DNA sequence, e.g., to insert an object (e.g., heterologous) nucleic acid sequence into a target genome, e.g., a mammalian genome, by reverse transcription. Such modularized and modified nucleic acids, polypeptide compositions and systems are described herein and are referred to as GENE WRITER™ gene editors. A GENE WRITER™ gene editor system comprises: (A) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain, and either (x) an endonuclease domain that contains DNA binding functionality or (y) an endonuclease domain and separate DNA binding domain; and (B) a template RNA comprising (i) a sequence that binds the polypeptide and (ii) a heterologous insert sequence. For example, the GENE WRITER™ genome editor protein may comprise a DNA-binding domain, a reverse transcriptase domain, and an endonuclease domain. In other embodiments, the GENE WRITER™ genome editor protein may comprise a reverse transcriptase domain and an endonuclease domain. In certain embodiments, the elements of the GENE WRITER™ gene editor polypeptide can be derived from sequences of non-LTR retrotransposons, e.g., APE-type or RLE-type retrotransposons or portions or domains thereof. In some embodiments the RLE-type non-LTR retrotransposon is from the R2, NeSL, HERO, R4, or CRE clade. In some embodiments the GENE WRITER™ genome editor is derived from R4 element X4_Line, which is found in the human genome. In some embodiments the APE-type non-LTR retrotransposon is from the R1, or Tx1 clade. In some embodiments the GENE WRITER™ genome editor is derived from Tx1 element Mare6, which is found in the human genome. The RNA template element of a GENE WRITER™ gene editor system is typically heterologous to the polypeptide element and provides an object sequence to be inserted (reverse transcribed) into the host genome. In some embodiments the GENE WRITER™ genome editor protein is capable of target primed reverse transcription.

In some embodiments the GENE WRITER™ genome editor is combined with a second polypeptide. In some embodiments the second polypeptide is derived from an APE-type non-LTR retrotransposon. In some embodiments the second polypeptide has a zinc knuckle-like motif. In some embodiments the second polypeptide is a homolog of Gag proteins.

Polypeptide Component of GENE WRITER™ Gene Editor System

RT Domain:

In certain aspects of the present invention, the reverse transcriptase domain of the GENE WRITER™ system is based on a reverse transcriptase domain of an APE-type or RLE-type non-LTR retrotransposon. A wild-type reverse transcriptase domain of an APE-type or RLE-type non-LTR retrotransposon can be used in a GENE WRITER™ system or can be modified (e.g., by insertion, deletion, or substitution of one or more residues) to alter the reverse transcriptase activity for target DNA sequences. In some embodiments the reverse transcriptase is altered from its natural sequence to have altered codon usage, e.g. improved for human cells. In some embodiments the reverse transcriptase domain is a heterologous reverse transcriptase from a different retrovirus, LTR-retrotransposon, or non-LTR retrotransposon. In certain embodiments, a GENE WRITER™ system includes a polypeptide that comprises a reverse transcriptase domain of an RLE-type non-LTR retrotransposon from the R2, NeSL, HERO, R4, or CRE clade, or of an APE-type non-LTR retrotransposon from the R1, or Tx1 clade. In certain embodiments, a GENE WRITER™ system includes a polypeptide that comprises a reverse transcriptase domain of a retrotransposon listed in Table 1, Table 2, or Table 3. In embodiments, the amino acid sequence of the reverse transcriptase domain of a GENE WRITER™ system is at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identical to the amino acid sequence of a reverse transcriptase domain of a retrotransposon whose DNA sequence is referenced in Table 1, Table 2, or Table 3. A person having ordinary skill in the art is capable of identifying reverse transcription domains based upon homology to other known reverse transcription domains using routine tools as Basic Local Alignment Search Tool (BLAST). In some embodiments, reverse transcriptase domains are modified, for example by site-specific mutation. In embodiments, the reverse transcriptase domain is engineered to bind a heterologous template RNA.

Endonuclease Domain:

In certain embodiments, the endonuclease/DNA binding domain of an APE-type retrotransposon or the endonuclease domain of an RLE-type retrotransposon can be used or can be modified (e.g., by insertion, deletion, or substitution of one or more residues) in a GENE WRITER™ system described herein. In some embodiments the endonuclease domain or endonuclease/DNA binding domain is altered from its natural sequence to have altered codon usage, e.g. improved for human cells. In some embodiments the endonuclease element is a heterologous endonuclease element, such as Fok1 nuclease, a type-II restriction 1-like endonuclease (RLE-type nuclease), or another RLE-type endonuclease (also known as REL). In some embodiments the heterologous endonuclease activity has nickase activity and does not form double stranded breaks. The amino acid sequence of an endonuclease domain of a GENE WRITER™ system described herein may be at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identical to the amino acid sequence of an endonuclease domain of a retrotransposon whose DNA sequence is referenced in Table 1, 2, or 3. A person having ordinary skill in the art is capable of identifying endounclease domains based upon homology to other known endonuclease domains using tools as Basic Local Alignment Search Tool (BLAST). In certain embodiments, the heterologous endonuclease is Fok1 or a functional fragment thereof. In certain embodiments, the heterologous endonuclease is a Holliday junction resolvase or homolog thereof, such as the Holliday junction resolving enzyme from Sulfolobus solfataricus-Ssol Hje (Govindaraju et al., Nucleic Acids Research 44:7, 2016). In certain embodiments, the heterologous endonuclease is the endonuclease of the large fragment of a spliceosomal protein, such as Prp8 (Mahbub et al., Mobile DNA 8:16, 2017). For example, a GENE WRITER™ polypeptide described herein may comprise a reverse transcriptase domain from an APE- or RLE-type retrotransposon and an endonuclease domain that comprises Fok1 or a functional fragment thereof. In still other embodiments, homologous endonuclease domains are modified, for example by site-specific mutation, to alter DNA endonuclease activity. In still other embodiments, endonuclease domains are modified to remove any latent DNA-sequence specificity.

DNA Binding Domain:

In certain aspects, the DNA-binding domain of a GENE WRITER™ polypeptide described herein is selected, designed, or constructed for binding to a desired host DNA target sequence. In certain embodiments, the DNA-binding domain of the engineered RLE is a heterologous DNA-binding protein or domain relative to a native retrotransposon sequence. In some embodiments the heterologous DNA binding element is a zinc-finger element or a TAL effector element, e.g., a zinc-finger or TAL polypeptide or functional fragment thereof. In some embodiments the heterologous DNA binding element is a sequence-guided DNA binding element, such as Cas9, Cpf1, or other CRISPR-related protein that has been altered to have no endonuclease activity. In some embodiments the heterologous DNA binding element retains endonuclease activity. In some embodiments the heterologous DNA binding element replaces the endonuclease element of the polypeptide. In specific embodiments, the heterologous DNA-binding domain can be any one or more of Cas9, TAL domain, ZF domain, Myb domain, combinations thereof, or multiples thereof. In certain embodiments, the heterologous DNA-binding domain is a DNA binding domain of a retrotransposon described in Table 1, Table 2, or Table 3. A person having ordinary skill in the art is capable of identifying DNA binding domains based upon homology to other known DNA binding domains using tools as Basic Local Alignment Search Tool (BLAST). In still other embodiments, DNA-binding domains are modified, for example by site-specific mutation, increasing or decreasing DNA-binding elements (for example, number and/or specificity of zinc fingers), etc., to alter DNA-binding specificity and affinity. In some embodiments the DNA binding domain is altered from its natural sequence to have altered codon usage, e.g. improved for human cells

In certain aspects of the present invention, the host DNA-binding site integrated into by the GENE WRITER™ system can be in a gene, in an intron, in an exon, an ORF, outside of a coding region of any gene, in a regulatory region of a gene, or outside of a regulatory region of a gene. In other aspects, the engineered RLE may bind to one or more than one host DNA sequence.

In certain embodiments, a GENE WRITER™ gene editor system RNA further comprises an intracellular localization sequence, e.g., a nuclear localization sequence. The nuclear localization sequence may be an RNA sequence that promotes the import of the RNA into the nucleus. In certain embodiments the nuclear localization signal is located on the template RNA. In certain embodiments, the retrotransposase polypeptide is encoded on a first RNA, and the template RNA is a second, separate, RNA, and the nuclear localization signal is located on the template RNA and not on an RNA encoding the retrotransposase polypeptide. While not wishing to be bound by theory, in some embodiments, the RNA encoding the retrotransposase is targeted primarily to the cytoplasm to promote its translation, while the template RNA is targeted primarily to the nucleus to promote its retrotransposition into the genome. In some embodiments the nuclear localization signal is at the 3′ end, 5′ end, or in an internal region of the template RNA. In some embodiments the nuclear localization signal is 3′ of the heterologous sequence (e.g., is directly 3′ of the heterologous sequence) or is 5′ of the heterologous sequence (e.g., is directly 5′ of the heterologous sequence). In some embodiments the nuclear localization signal is placed outside of the 5′ UTR or outside of the 3′ UTR of the template RNA. In some embodiments the nuclear localization signal is placed between the 5′ UTR and the 3′ UTR, wherein optionally the nuclear localization signal is not transcribed with the transgene (e.g., the nuclear localization signal is an anti-sense orientation or is downstream of a transcriptional termination signal or polyadenylation signal). In some embodiments the nuclear localization sequence is situated inside of an intron. In some embodiments a plurality of the same or different nuclear localization signals are in the RNA, e.g., in the template RNA. In some embodiments the nuclear localization signal is less than 5, 10, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900 or 1000 bp in legnth. Various RNA nuclear localization sequences can be used. For example, Lubelsky and Ulitsky, Nature 555 (107-111), 2018 describe RNA sequences which drive RNA localization into the nucleus. In some embodiments, the nuclear localization signal is a SINE-derived nuclear RNA localization (SIRLOIN) signal. In some embodiments the nuclear localization signal binds a nuclear-enriched protein. In some embodiments the nuclear localization signal binds the HNRNPK protein. In some embodiments the nuclear localization signal is rich in pyrimidines, e.g., is a C/T rich, C/U rich, C rich, T rich, or U rich region. In some embodiments the nuclear localization signal is derived from a long non-coding RNA. In some embodiments the nuclear localization signal is derived from MALAT1 long non-coding RNA or is the 600 nucleotide M region of MALAT1 (described in Miyagawa et al., RNA 18, (738-751), 2012). In some embodiments the nuclear localization signal is derived from BORG long non-coding RNA or is a AGCCC motif (described in Zhang et al., Molecular and Cellular Biology 34, 2318-2329 (2014). In some embodiments the nuclear localization sequence is described in Shukla et al., The EMBO Journal e98452 (2018). In some embodiments the nuclear localization signal is derived from a non-LTR retrotransposon, an LTR retrotransposon, retrovirus, or an endogenous retrovirus.

In certain embodiments, a GENE WRITER™ gene editor system polypeptide further comprises an intracellular localization sequence, e.g., a nuclear localization sequence and/or a nucleolar localization sequence. The nuclear localization sequence and/or nucleolar localization sequence may be amino acid sequences that promote the import of the protein into the nucleus and/or nucleolus, where it can promote integration of heterologous sequyence into the genome. In certain embodiments, a GENE WRITER™ gene editor system polypeptide (e.g., a retrotransposase, e.g., a polypeptide according to any of Tables 1, 2, or 3 herein) further comprises a nucleolar localization sequence. In certain embodiments, the retrotransposase polypeptide is encoded on a first RNA, and the template RNA is a second, separate, RNA, and the nucleolar localization signal is encoded on the RNA encoding the retrotransposase polypeptide and not on the template RNA. In some embodiments, the nucleolar localization signal is located at the N-terminus, C-terminus, or in an internal region of the polypeptide. In some embodiments, a plurality of the same or different nucleolar localization signals are used. In some embodiments, the nuclear localization signal is less than 5, 10, 25, 50, 75, or 100 amino acids in length. Various polypeptide nucleolar localization signals can be used. For example, Yang et al., Journal of Biomedical Science 22, 33 (2015), describe a nuclear localization signal that also functions as a nucleolar localization signal. In some embodiments, the nucleolar localization signal may also be a nuclear localization signal. In some embodiments, the nucleolar localization signal may overlap with a nuclear localization signal. In some embodiments, the nucleolar localization signal may comprise a stretch of basic residues. In some embodiments, the nucleolar localization signal may be rich in arginine and lysine residues. In some embodiments, the nucleolar localization signal may be derived from a protein that is enriched in the nucleolus. In some embodiments, the nucleolar localization signal may be derived from a protein enriched at ribosomal RNA loci. In some embodiments, the nucleolar localization signal may be derived from a protein that binds rRNA. In some embodiments, the nucleolar localization signal may be derived from MSP58. In some embodiments, the nucleolar localization signal may be a monopartite motif. In some embodiments, the nucleolar localization signal may be a bipartite motif. In some embodiments, the nucleolar localization signal may consist of a multiple monopartite or bipartite motifs. In some embodiments, the nucleolar localization signal may consist of a mix of monopartite and bipartite motifs. In some embodiments, the nucleolar localization signal may be a dual bipartite motif. In some embodiments, the nucleolar localization motif may be a KRASSQALGTIPKRRSSSRFIKRKK (SEQ ID NO: 1530). In some embodiments, the nucleolar localization signal may be derived from nuclear factor-KB-inducing kinase. In some embodiments, the nucleolar localization signal may be an RKKRKKK motif (SEQ ID NO: 1531) (described in Birbach et al., Journal of Cell Science, 117 (3615-3624), 2004).

In some embodiments, a nucleic acid described herein (e.g., an RNA encoding a GENE WRITER™ polypeptide, or a DNA encoding the RNA) comprises a microRNA binding site. In some embodiments, the microRNA binding site is used to increase the target-cell specificity of a GENE WRITER™ system. For instance, the microRNA binding site can be chosen on the basis that is is recognized by a miRNA that is present in a non-target cell type, but that is not present (or is present at a reduced level relative to the non-target cell) in a target cell type. Thus, when the RNA encoding the GENE WRITER™ polypeptide is present in a non-target cell, it would be bound by the miRNA, and when the RNA encoding the GENE WRITER™ polypeptide is present in a target cell, it would not be bound by the miRNA (or bound but at reduced levels relative to the non-target cell). While not wishing to be bound by theory, binding of the miRNA to the RNA encoding the GENE WRITER™ polypeptide may reduce production of the GENE WRITER™ polypeptide, e.g., by degrading the mRNA encoding the polypeptide or by interfering with translation. Accordingly, the heterologous object sequence would be inserted into the genome of target cells more efficiently than into the genome of non-target cells. A system having a microRNA binding site in the RNA encoding the GENE WRITER™ polypeptide (or encoded in the DNA encoding the RNA) may also be used in combination with a template RNA that is regulated by a second microRNA binding site, e.g., as described herein in the section entitled “Template RNA component of GENE WRITER™ gene editor system.”

TABLE 1
TABLE 1: APE-type non-LTR retrotransposon elements
	Sequence
Family	Accession	Mobile Element	Name	Organism
Dewa	AB097143	ORF2	Danio rerio retrotransposon	Danio rerio
			DewaDr1 DNA, complete sequence
HeT-A	KJ081250	non-LTR	Drosophila melanogaster non-LTR	Drosophila
		retrotransposon:	retrotransposon HeT-A, partial	melanogaster
		HeT-A	sequence
Keno	AB111948	ORF2	Tetraodon nigroviridis	Tetraodon
			retrotransposon KenoTn1 DNA,	nigroviridis
			partial sequence
KenoDr1;	AB097144	ORF2	Danio rerio retrotransposon KenoDr1	Danio rerio
Keno			DNA, complete sequence
KenoFr1;	AB111947	ORF2	Takifugu rubripes retrotransposon	Takifugu
Keno			KenoFr1 DNA, complete sequence	rubripes
Kibi	AB097139	ORF2	Danio rerio retrotransposon KibiDr2	Danio rerio
			DNA, complete sequence
Kibi	AB097138	ORF2	Danio rerio retrotransposon KibiDr1	Danio rerio
			DNA, complete sequence
Kibi	AB097137	ORF2	Tetraodon nigroviridis	Tetraodon
			retrotransposon KibiTn1 DNA,	nigroviridis
			complete sequence
Kibi	AB097136	ORF2	Takifugu rubripes retrotransposon	Takifugu
			KibiFr1 DNA, complete sequence	rubripes
KoshiTn1	AB097135	ORF2	Tetraodon nigroviridis	Tetraodon
			retrotransposon KoshiTn1 DNA,	nigroviridis
			complete sequence
Mutsu	AB097142	ORF2	Danio rerio retrotransposon	Danio rerio
			MutsuDr3 DNA, partial sequence
Mutsu	AB097141	ORF2	Danio rerio retrotransposon	Danio rerio
			MutsuDr2 DNA, partial sequence
Mutsu	AB097140	ORF2	Danio rerio retrotransposon	Danio rerio
			MutsuDr1 DNA, complete sequence
R1	HQ284568	non-LTR	Trilocha sp. GAS-2011 isolate TrilSp.6	Trilocha
		retrotransposon:	non-LTR retrotransposon R1-like	sp. GAS-2011
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284534	non-LTR	Scopula ornata isolate ScoOrn.6 non-	Scopula ornata
		retrotransposon:	LTR retrotransposon R1-like reverse
		R1-like	transcriptase gene, partial cds
R1	HQ284496	non-LTR	Perigonia ilus isolate PerIlus.31 non-	Perigonia ilus
		retrotransposon:	LTR retrotransposon R1-like reverse
		R1-like	transcriptase gene, partial cds
R1	HQ284489	non-LTR	Oxytenis modestia isolate	Oxytenis
		retrotransposon:	OxyMod.2_3_4_7_9 non-LTR	modestia
		R1-like	retrotransposon R1-like reverse
			transcriptase gene, partial cds
R1	HQ284488	non-LTR	Oxytenis modestia isolate OxyMod.1	Oxytenis
		retrotransposon:	non-LTR retrotransposon R1-like	modestia
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284476	non-LTR	Oeneis magna dubia isolate	Oeneis magna
		retrotransposon:	OenMag.26 non-LTR retrotransposon	dubia
		R1-like	R1-like reverse transcriptase-like
			gene, partial sequence
R1	HQ284437	non-LTR	Lymantria dispar isolate LymDis.2	Lymantria
		retrotransposon:	non-LTR retrotransposon R1-like	dispar
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284435	non-LTR	Lymantria dispar isolate LymDis.1	Lymantria
		retrotransposon:	non-LTR retrotransposon R1-like	dispar
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284432	non-LTR	Janiodes laverna isolate JanLav.911	Janiodes
		retrotransposon:	non-LTR retrotransposon R1-like	laverna
		R1-like	reverse transcriptase-like gene,
			partial sequence
R1	HQ284431	non-LTR	Janiodes laverna isolate JanLav.811	Janiodes
		retrotransposon:	non-LTR retrotransposon R1-like	laverna
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284430	non-LTR	Janiodes laverna isolate JanLav.5	Janiodes
		retrotransposon:	non-LTR retrotransposon R1-like	laverna
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284428	non-LTR	Janiodes laverna isolate JanLav.411	Janiodes
		retrotransposon:	non-LTR retrotransposon R1-like	laverna
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284426	non-LTR	Janiodes laverna isolate JanLav.211	Janiodes
		retrotransposon:	non-LTR retrotransposon R1-like	laverna
		R1-like	reverse transcriptase-like gene,
			partial sequence
R1	HQ284421	non-LTR	Heteropterus morpheus isolate	Heteropterus
		retrotransposon:	HetMor.3 non-LTR retrotransposon	morpheus
		R1-like	R1-like reverse transcriptase gene,
			partial cds
R1	HQ284402	non-LTR	Erinnyis ello isolate EriEllo.22 non-	Erinnyis ello
		retrotransposon:	LTR retrotransposon R1-like reverse
		R1-like	transcriptase-like gene, partial
			sequence
R1	HQ284399	non-LTR	Erebia theano isolate EreThe.29 non-	Erebia theano
		retrotransposon:	LTR retrotransposon R1-like reverse
		R1-like	transcriptase gene, partial cds
R1	HQ284398	non-LTR	Erebia theano isolate EreThe.28 non-	Erebia theano
		retrotransposon:	LTR retrotransposon R1-like reverse
		R1-like	transcriptase-like gene, partial
			sequence
R1	HQ284397	non-LTR	Erebia theano isolate EreThe.27 non-	Erebia theano
		retrotransposon:	LTR retrotransposon R1-like reverse
		R1-like	transcriptase-like gene, partial
			sequence
R1	HQ284391	non-LTR	Emesis lucinda isolate EmeLuc.23	Emesis lucinda
		retrotransposon:	non-LTR retrotransposon R1-like
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284390	non-LTR	Emesis lucinda isolate EmeLuc.2 non-	Emesis lucinda
		retrotransposon:	LTR retrotransposon R1-like reverse
		R1-like	transcriptase gene, partial cds
R1	HQ284364	non-LTR	Coenonympha glycerion isolate	Coenonympha
		retrotransposon:	CoeGly.9 non-LTR retrotransposon	glycerion
		R1-like	R1-like reverse transcriptase gene,
			partial cds
R1	HQ284363	non-LTR	Coenonympha glycerion isolate	Coenonympha
		retrotransposon:	CoeGly.8 non-LTR retrotransposon	glycerion
		R1-like	R1-like reverse transcriptase-like
			gene, partial sequence
R1	HQ284362	non-LTR	Coenonympha glycerion isolate	Coenonympha
		retrotransposon:	CoeGly.7 non-LTR retrotransposon	glycerion
		R1-like	R1-like reverse transcriptase gene,
			partial cds
R1	HQ284361	non-LTR	Coenonympha glycerion isolate	Coenonympha
		retrotransposon:	CoeGly.5 non-LTR retrotransposon	glycerion
		R1-like	R1-like reverse transcriptase-like
			gene, partial sequence
R1	HQ284357	non-LTR	Coenonympha glycerion isolate	Coenonympha
		retrotransposon:	CoeGly.13 non-LTR retrotransposon	glycerion
		R1-like	R1-like reverse transcriptase gene,
			partial cds
R1	HQ284356	non-LTR	Coenonympha glycerion isolate	Coenonympha
		retrotransposon:	CoeGly.11 non-LTR retrotransposon	glycerion
		R1-like	R1-like reverse transcriptase-like
			gene, partial sequence
R1	HQ284350	non-LTR	Catocyclotis adelina isolate	Catocyclotis
		retrotransposon:	CatAde.18 non-LTR retrotransposon	adelina
		R1-like	R1-like reverse transcriptase gene,
			partial cds
R1	HQ284340	non-LTR	Caria rhacotis isolate CarRha.11 non-	Caria rhacotis
		retrotransposon:	LTR retrotransposon R1-like reverse
		R1-like	transcriptase gene, partial cds
R1	HQ284339	non-LTR	Caria rhacotis isolate CarRha.1 non-	Caria rhacotis
		retrotransposon:	LTR retrotransposon R1-like reverse
		R1-like	transcriptase gene, partial cds
R1	HQ284319	non-LTR	Archiearis parthenias isolate BrePar.1	Archiearis
		retrotransposon:	non-LTR retrotransposon R1-like	parthenias
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284318	non-LTR	Brangas neora isolate BraNeo.32	Brangas neora
		retrotransposon:	non-LTR retrotransposon R1-like
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284292	non-LTR	Araschnia levana isolate AraLev.31	Araschnia levana
		retrotransposon:	non-LTR retrotransposon R1-like
		R1-like	reverse transcriptase-like gene,
			partial sequence
R1	HQ284286	non-LTR	Araschnia levana isolate AraLev.1	Araschnia levana
		retrotransposon:	non-LTR retrotransposon R1-like
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284280	non-LTR	Anteros formosus isolate AntForm.34	Anteros
		retrotransposon:	non-LTR retrotransposon R1-like	formosus
		R1-like	reverse transcriptase gene, partial
			cds
R1	HQ284279	non-LTR	Anteros formosus isolate AntForm.32	Anteros
		retrotransposon:	non-LTR retrotransposon R1-like	formosus
		R1-like	reverse transcriptase-like gene,
			partial sequence
R1	HQ284278	non-LTR	Anteros formosus isolate AntForm.31	Anteros
		retrotransposon:	non-LTR retrotransposon R1-like	formosus
		R1-like	reverse transcriptase-like gene,
			partial sequence
R1	HQ284270	non-LTR	Agrotis exclamationis isolate	Agrotis
		retrotransposon:	AgrExcl.27 non-LTR retrotransposon	exclamationis
		R1-like	R1-like reverse transcriptase gene,
			partial cds
R1	HQ284267	non-LTR	Agrius cingulata isolate	Agrius
		retrotransposon:	AgrCing.36_39 non-LTR	cingulata
		R1-like	retrotransposon R1-like reverse
			transcriptase gene, partial cds
R1	HQ284266	non-LTR	Agrius cingulata isolate AgrCing.3	Agrius
		retrotransposon:	non-LTR retrotransposon R1-like	cingulata
		R1-like	reverse transcriptase-like gene,
			partial sequence
R1	HQ284263	non-LTR	Aglia tau isolate AglTau.8 non-LTR	Aglia tau
		retrotransposon:	retrotransposon R1-like reverse
		R1-like	transcriptase gene, partial cds
R1	HQ284262	non-LTR	Aglia tau isolate AglTau.7 non-LTR	Aglia tau
		retrotransposon:	retrotransposon R1-like reverse
		R1-like	transcriptase gene, partial cds
R1	DQ836362	MalR1	Maculinea alcon R1-like non-LTR	Phengaris alcon
			retrotransposon R1 reverse
			transcriptase (RT) pseudogene,
			partial sequence
R1	DQ836391	MnaR1	Maculinea nausithous R1-like non-	Phengaris
			LTR retrotransposon R1 reverse	nausithous
			transcriptase (RT) gene, partial cds
R1	KU543683	non-LTR	Bactrocera tryoni clone Btry_5404	Bactrocera
		retrotransposon	non-LTR retrotransposon R1,	tryoni
		and non-LTR	complete sequence
		retrovirus
		reverse
		transcriptase;
		Region: RT_nLTR
R1	KU543682	non-LTR	Bactrocera tryoni clone Btry_5167	Bactrocera
		retrotransposon	non-LTR retrotransposon R1,	tryoni
		and non-LTR	complete sequence
		retrovirus
		reverse
		transcriptase;
		Region: RT_nLTR
R1	KU543679	non-LTR	Bactrocera tryoni clone Btry_4956	Bactrocera
		retrotransposon	non-LTR retrotransposon R1,	tryoni
		and non-LTR	complete sequence
		retrovirus
		reverse
		transcriptase;
		Region: RT_nLTR
R1	KU543678	non-LTR	Bactrocera tryoni clone Btry_5979	Bactrocera
		retrotransposon	non-LTR retrotransposon R1,	tryoni
		and non-LTR	complete sequence
		retrovirus
		reverse
		transcriptase;
		Region: RT_nLTR
R1	AB078933	ORF1	Papilio xuthus non-LTR	Papilio xuthus
			retrotransposon gene for gag-like
			protein, partial cds, clone: SARTPx2-2
R1	AB078932	ORF1	Papilio xuthus non-LTR	Papilio xuthus
			retrotransposon gene for gag-like
			protein, partial cds, clone: SARTPx2-1
R1	AB078936	ORF2	Papilio xuthus non-LTR	Papilio xuthus
			retrotransposon genes for gag-like
			protein, reverse transcriptase, partial
			cds, clone: SARTPx4-N18
R1	AB078935	ORF2	Papilio xuthus non-LTR	Papilio xuthus
			retrotransposon genes for gag-like
			protein, reverse transcriptase, partial
			and complete cds, clone: SARTPx3-N7
R1	AB078934	ORF2	Papilio xuthus non-LTR	Papilio xuthus
			retrotransposon genes for gag-like
			protein, reverse transcriptase, partial
			cds, clone: SARTPx3-N3
R1	AB078931	ORF2	Papilio xuthus non-LTR	Papilio xuthus
			retrotransposon genes for gag-like
			protein, reverse transcriptase, partial
			and complete cds, clone: SARTPx1-N14
R1	AB078930	ORF2	Papilio xuthus non-LTR	Papilio xuthus
			retrotransposon genes for gag-like
			protein, reverse transcriptase, partial
			and complete cds, clone: SARTPx1-N5
R1	AB078929	ORF2	Papilio xuthus non-LTR	Papilio xuthus
			retrotransposon genes for gag-like
			protein, reverse transcrpitase, partial
			and complete cds, clone: SARTPx1-N4
R1	AB078928	ORF2	Papilio xuthus non-LTR	Papilio xuthus
			retrotransposon gene for gag-like
			protein, reverse transcrpitase,
			complete and partial cds, clone:
			SARTPx1-3
R1	KP771712	ORF2; contains	Blattella germanica non-LTR	Blattella
		endonuclease,	retrotransposon TRAS-like 2,	germanica
		reverse	complete sequence
		transcriptase
		and RNaseH
R1	KP771711	ORF2; contains	Blattella germanica non-LTR	Blattella
		endonuclease,	retrotransposon TRAS-like 1,	germanica
		reverse	complete sequence
		transcriptase
		and RNaseH
R1	AF015813	R1 ORF	Dugesiella sp. retrotransposon R1	Aphonopelma
			reverse transcriptase gene, partial	sp. WDB-1998
			cds
R1	AF015489	R1 ORF	Dugesiella sp. retrotransposon R1	Aphonopelma
			reverse transcriptase gene, partial	sp. WDB-1998
			cds
R1Bm	AB182560	non-LTR	Bombyx mori genes for non-LTR	Bombyx mori
		retrotransposon	retrotransposon R1Bmks ORF1
		R1Bmks ORF2	protein, non-LTR retrotransposon
			R1Bmks ORF2 protein, complete cds
R6	AB090819	ORF2	Anopheles gambiae retrotransposon	Anopheles
			R6Ag3 DNA, complete sequence	gambiae
R6	AB090818	ORF2	Anopheles gambiae retrotransposon	Anopheles
			R6Ag2 DNA, complete sequence	gambiae
R6	AB090817	ORF2	Anopheles gambiae retrotransposon	Anopheles
			R6Ag1 DNA, complete sequence	gambiae
R6	KJ958615	R2	Bacillus rossius non-LTR	Bacillus
			retrotransposon reVIR6, partial	rossius
			sequence
R6	KJ958596	R2	Bacillus rossius non-LTR	Bacillus
			retrotransposon reBER6, partial	rossius
			sequence
R6	AF352480	transposon:	Chironomus circumdatus clone cir6	Chironomus
		NLRCth1-	transposon NLRCth1-like non-LTR	circumdatus
		like non-LTR	retrotransposon reverse
		retrotransposon	transcriptase gene, partial cds
R6	AF373367	transposon:	Clelia rustica clone CR6 non-LTR	Paraphimophis
		non-LTR	retrotransposon LINE2 reverse	rusticus
		retrotransposon	transcriptase pseudogene, partial
		LINE2	sequence
R7	AB090820	ORF2	Anopheles gambiae retrotransposon	Anopheles
			R7Ag1 DNA, complete sequence	gambiae
R7	AB090821	ORF2	Anopheles gambiae retrotransposon	Anopheles
			R7Ag2 DNA, complete sequence	gambiae
R7	KJ958622	R2	Bacillus rossius non-LTR	Bacillus
			retrotransposon trKOR7, partial	rossius
			sequence
R7	KJ958616	R2	Bacillus rossius non-LTR	Bacillus
			retrotransposon reVIR7, partial	rossius
			sequence
R7	KJ958597	R2	Bacillus rossius non-LTR	Bacillus
			retrotransposon reBER7, partial	rossius
			sequence
R7	AF352514	transposon:	Chironomus circumdatus clone cir7	Chironomus
		NLRCth1-like	transposon NLRCth1-like non-LTR	circumdatus
		non-LTR	retrotransposon reverse
		retrotransposon	transcriptase pseudogene, partial
			sequence
Rt2	AY379084	truncated;	Leptocheirus plumulosus	Leptocheirus
		similar to	retrotransposon LpRt2, partial	plumulosus
		reverse	sequence
		transcriptase
Rt2	MSQRT2RET		Anopheles gambiae retrotransposon	Anopheles
			RT2, complete sequence	gambiae
RTAg4	AB090813	ORF2	Anopheles gambiae retrotransposon	Anopheles
			RTAg4 DNA, complete sequence	gambiae
TRAS1	BMOTRAS1	DNA binding	Bombyx mori gene, complete	Bombyx mori
		domain at	sequence of retrotransposon TRAS1
		AA1103-1120.
TRAS3	JX875955	similar to	Acyrthosiphon pisum clone LSR1 non-	Acyrthosiphon
		reverse	LTR retrotransposon TRAS3,	pisum
		transcriptases	complete sequence
Tx1	AJ621359	transposon:	Tetraodon nigroviridis non-LTR	Tetraodon
		non-LTR	retrotransposon TX1-1_Tet, complete	nigroviridis
		retrotransposon	sequence
		TX1-1_Tet
Tx1	AJ621360	transposon:	Tetraodon nigroviridis partial non-	Tetraodon
		non-LTR	LTR retrotransposon TX1-2_Tet	nigroviridis
		retrotransposon
		TX1-2_Tet
Tx1	AJ621361	transposon:	Tetraodon nigroviridis partial non-	Tetraodon
		non-LTR	LTR retrotransposon TX1-3_Tet	nigroviridis
		retrotransposon
		TX1-3_Tet
Tx1	AJ621362	transposon:	Tetraodon nigroviridis partial non-	Tetraodon
		non-LTR	LTR retrotransposon TX1-4_Tet	nigroviridis
		retrotransposon
		TX1-4_Tet
Tx1	DQ118004	transposon:	Acipenser ruthenus clone dg194	Acipenser
		Tx1-like	transposon Tx1-like retrotransposon	ruthenus
		retrotransposon	Tx1Aru reverse transcriptase-like
		Tx1Aru	gene, partial sequence
Tx1	AB097134	ORF2	Takifugu rubripes retrotransposon	Takifugu
			KoshiFr1 DNA, complete sequence	rubripes
Tx1	AB090816	ORF2	Anopheles gambiae retrotransposon	Anopheles
			MinoAg1 DNA, complete sequence	gambiae
Tx1	AB090812	ORF2	Anopheles gambiae retrotransposon	Anopheles
			RTAg3 DNA, complete sequence	gambiae
Waldo	AH009917	non-LTR	Drosophila melanogaster Waldo-A	Drosophila
		retrotransposon:	non-LTR retrotransposon, 5′	melanogaster
		Waldo-A	sequence
Waldo	AH009916	non-LTR	Drosophila melanogaster clone CBE9	Drosophila
		retrotransposon:	Waldo-A non-LTR retrotransposon, 5′	melanogaster
		Waldo-A	sequence
Waldo	AH009915	non-LTR	Drosophila melanogaster Waldo-A	Drosophila
		retrotransposon:	non-LTR retrotransposon, 5′	melanogaster
		Waldo-A	sequence
Waldo	AH009914	non-LTR	Drosophila melanogaster Waldo-A	Drosophila
		retrotransposon:	non-LTR retrotransposon	melanogaster
		Waldo-A
Waldo	AH009920	non-LTR	Drosophila melanogaster Waldo-B	Drosophila
		retrotransposon:	non-LTR retrotransposon, 5′	melanogaster
		Waldo-B	sequence
Waldo	AH009919	non-LTR		Drosophila
		retrotransposon:		melanogaster
		Waldo-B
Waldo	AH009918	non-LTR		Drosophila
		retrotransposon:		melanogaster
		Waldo-B
Waldo	AB090815	ORF2	Anopheles gambiae retrotransposon	Anopheles
			WaldoAg2 DNA, complete sequence	gambiae
Waldo	AB090814	ORF2	Anopheles gambiae retrotransposon	Anopheles
			WaldoAg1 DNA, complete sequence	gambiae
Waldo	AB078939	ORF2	Forficula scudderi non-LTR	Forficula
			retrotransposon pseudogene for	scudderi
			reverse transcriptase, clone:
			WaldoFs1-26
Waldo	AB078938	ORF2	Forficula scudderi non-LTR	Forficula
			retrotransposon pseudogene for	scudderi
			reverse transcriptase, clone:
			WaldoFs1-2
Waldo	AB078937	ORF2	Forficula scudderi non-LTR	Forficula
			retrotransposon pseudogene for	scudderi
			reverse transcriptase, clone:
			WaldoFs1-1

TABLE 2
TABLE 2: RLE-type non-LTR retrotransposon elements
Family	Accession	Mobile Element	Name/Description	Organism
CRE	EF067892		Colletotrichum cereale	Colletotrichum
			clone 9F8-1558 Ccret3 non-LTR	cereale
			retrotransposon, partial sequence
CRE	EF067894		Colletotrichum cereale	Colletotrichum
			clone 9F8-2137 Ccret3 non-LTR	cereale
			retrotransposon, partial sequence
CRE	MG028000	non-LTR	Characidium gomesi voucher	Characidium
		retrotransposon:	MNRJ20998 non-LTR	gomesi
		Rex3	retrotransposon Rex3, partial
			sequence
CRE	KY566213	non-LTR	Characidium gomesi non-LTR	Characidim
		retrotransposon:	retrotransposon Rex3, partial	gomesi
		Rex3	sequence
CRE	GU949558		Kalotermes flavicollis	Kalotermes
			isolate Crete non-LTR	flavicollis
			retrotransposon R2, complete
			sequence; and R2 protein
			gene, complete cds
CRE;	CFU19151	poly dA	Crithidia fasciculata	Crithidia
CRE2		tracts in	retrotransposon CRE2 in mini-	fasciculata
		5′ and	exon gene, putative reverse
		3′ UTRs	transcriptase gene, complete cds
CZAR	BR000987	pol	TPA_inf: Capsaspora owczarzaki	Capsaspora
			DNA, non-LTR retrotransposon	owczarzaki
			CoL4, complete sequence,
			strain: ATCC 30864
CZAR	BR000986	pol	TPA_inf: Capsaspora owczarzaki	Capsaspora
			DNA, non-LTR retrotransposon	owczarzaki
			CoL3, complete sequence,
			strain: ATCC 30864
CZAR	BR000985	pol	TPA_inf: Capsaspora owczarzaki	Capsaspora
			DNA, non-LTR retrotransposon	owczarzaki
			CoL2, complete sequence,
			strain: ATCC 30864
CZAR	BR000984	pol	TPA_inf: Capsaspora owczarzaki	Capsaspora
			DNA, non-LTR retrotransposon	owczarzaki
			CoL1, complete sequence,
			strain: ATCC 30864
DongAG;	AB097127	rt	Anopheles gambiae	Anopheles
Dong			retrotransposon DongAg DNA,	gambiae
			partial sequence
EhRLE2	AB097128	rt	Entamoeba histolytica	Entamoeba
			retrotransposon EhRLE2 DNA,	histolytica
			complete sequence
EhRLE3	AB097129	rt	Entamoeba histolytica	Entamoeba
			retrotransposon EhRLE3 DNA,	histolytica
			complete sequence
Genie	AF440196	endonuclease	Giardia intestinalis non-LTR	Giardia
			retrotransposon GENIE 1 pol	intestinalis
			polyprotein gene, complete cds
Genie	BK000097	endonuclease	TPA_exp: Giardia intestinalis	Giardia
			non-LTR retrotransposon Genie	intestinalis
			1A gene, partial sequence
Genie	BK000095	endonuclease	TPA_exp: Giardia intestinalis	Giardia
			non-LTR retrotransposon Genie	intestinalis
			1 gene, partial sequence
Genie	BK000096	insertion site	TPA_exp: Giardia intestinalis	Giardia
		for non-LTR	non-LTR retrotransposon Genie	intestinalis
		retrotransposon	1 target site sequence
		Genie 1
Genie	AY216701	non-	Girardia tigrina GENIE	Girardia
		experimental	retrotransposon, complete	tigrina
		evidence, no	sequence
		additional
		details
		recorded
Genie	BK000098	similar to	TPA_exp: Giardia intestinalis	Giardia
		endonuclease	non-LTR retrotransposon Genie	intestinalis
			2 gene, complete sequence
GilD	AF433877	(tca)n (SEQ	Giardia intestinalis inactive	Giardia
		ID NO: 1532)	non-LTR retrotransposon GilD,	intestinalis
		or (tga)n	consensus sequence
		(SEQ ID NO:
		1533), n = 2-4
GilM	AF433875	poly(dA)	Giardia intestinalis non-LTR	Giardia
		tract	LINE-like retrotransposon	intestinalis
			GilM, complete sequence
Hero	AB097132	rt	Danio rerio retrotransposon	Danio rerio
			HERODr DNA, complete sequence
Hero	AB097130	rt	Takifugu rubripes	Takifugu rubripes
			retrotransposon HEROFr DNA,
			complete sequence
HEROTn	AB097131	rt	Tetraodon nigroviridis	Tetraodon
			retrotransposon HEROTn DNA,	nigroviridis
			complete sequence
NeSL_3_135_68117	FJ905846	non-LTR	Daphnia pulex non-LTR	Daphnia pulex
		retrotransposon:	retrotransposon
		NeSL_3_135_68117	NeSL_3_135_68117, complete
			sequence
NeSL;	DQ099731	target site	Caenorhabditis briggsae	Caenorhabditis
NeSL-1		duplication	transposon NeSl-1-like non-LTR	briggsae
			retrotransposon NeSL-1Cb
			reverse transcriptase (pol)
			gene, complete cds
PERERE-9	BN000800		TPA_exp: Schistosoma mansoni	Schistosoma
			Perere-9 non-LTR	mansoni
			retrotransposon
R2	AF015814	R2	Limulus polyphemus	Limulus
			retrotransposon R2, complete	polyphemus
			sequence
R2	AF090145	R2	Nasonia vitripennis R2 non-LTR	Nasonia
			retrotransposable element	vitripennis
			reverse transcriptase gene,
			partial cds
R2	AF015818	R2	Porcellio scaber	Porcellio scaber
			retrotransposon R2, complete
			sequence
R2	AF015815	R2	Anurida maritima	Anurida maritima
			retrotransposon R2, complete
			sequence
R2	M16558	R2	Bombyx mori rDNA insertion	Bombyx mori
			element R2 (typeII), complete cds
R2	AF015819	R2	Forficula auricularia	Forficula
			retrotransposon R2, complete	auricularia
			sequence.
R2	EU854578	R2	Triops cancriformis non-LTR	Triops
			retrotransposon R2 reverse	cancriformis
			transcriptase gene, complete cds
R2	GU949555	R2	Reticulitermes lucifugus	Reticulitermes
			non-LTR retrotransposon R2,	lucifugus
			complete sequence; and R2
			protein gene, complete cds
R2	AB097123	rt	Ciona intestinalis	Ciona intestinalis
			retrotransposon R2Ci-C DNA,
			partial sequence
R2	AB097124	rt	Ciona intestinalis	Ciona intestinalis
			retrotransposon R2Ci-D DNA,
			partial sequence
R2	FJ461304	R2	Rhynchosciara americana	Rhynchosciara
			non-LTR retrotransposon RaR2	americana
			reverse transcriptase gene,
			complete cds
R2	AB097121	rt	Ciona intestinalis	Ciona intestinalis
			retrotransposon R2Ci-A DNA,
			complete sequence
R2	KP657892	R2	Bacillus rossius isolate	Bacillus rossius
			roCAP(full).9 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657890	R2	Bacillus rossius isolate	Bacillus rossius
			roCAP(full).7 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657888	R2	Bacillus rossius isolate	Bacillus rossius
			roCAP(full).5 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657870	R2	Bacillus rossius isolate	Bacillus rossius
			roCAP(full).1 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657833	R2	Bacillus rossius isolate	Bacillus rossius
			roANZ(full).13 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657832	R2	Bacillus rossius isolate	Bacillus rossius
			roANZ(full).12 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657830	R2	Bacillus rossius isolate	Bacillus rossius
			roANZ(full).10 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657807	R2	Bacillus rossius isolate	Bacillus rossius
			roANZ(−101).8 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657806	R2	Bacillus rossius isolate	Bacillus rossius
			roANZ(−101).7 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657805	R2	Bacillus rossius isolate	Bacillus rossius
			roANZ(−101).6 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657802	R2	Bacillus rossius isolate	Bacillus rossius
			roANZ(−101).3 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657799	R2	Bacillus rossius isolate	Bacillus rossius
			roANZ(−101).1 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	FJ461304	R2	Rhynchosciara americana	Rhynchosciara
			non-LTR retrotransposon RaR2	americana
			reverse transcriptase gene,
			complete cds
R2	JQ082370	polyA_signal_sequence	Eyprepocnemis plorans non-LTR	Eyprepocnemis
			retrotransposon R2 R2	plorans
			protein gene, complete cds
R2	KJ958672	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCUR4_deg,
			partial sequence
R2	KJ958671	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCUR3_deg,
			partial sequence
R2	KJ958670	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCUR2_deg,
			partial sequence
R2	KJ958669	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCUR1_deg,
			partial sequence
R2	KJ958668	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCDF6_deg,
			partial sequence
R2	KJ958667	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCDF5_deg,
			partial sequence
R2	KJ958666	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCDF4_deg,
			partial sequence
R2	KJ958665	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCDF3_deg,
			partial sequence
R2	KJ958664	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCDF2_deg,
			partial sequence
R2	KJ958663	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCDF1_deg,
			partial sequence
R2	KJ958662	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCOM10_deg,
			partial sequence
R2	KJ958661	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCOM5_deg,
			partial sequence
R2	KJ958660	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCOM7_deg,
			partial sequence
R2	KJ958659	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCOM3_deg,
			partial sequence
R2	KJ958658	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCOM2_deg,
			partial sequence
R2	KJ958657	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reMSN6_deg,
			partial sequence
R2	KJ958656	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reMSN5_deg,
			partial sequence
R2	KJ958655	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reMSN4_deg,
			partial sequence
R2	KJ958654	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reMSN3_deg,
			partial sequence
R2	KJ958653	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reMSN2_deg,
			partial sequence
R2	KJ958652	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reMSN1_deg,
			partial sequence
R2	KJ958651	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon rePAT8_deg,
			partial sequence
R2	KJ958650	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon rePAT7_deg,
			partial sequence
R2	KJ958649	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon rePAT6_deg,
			partial sequence
R2	KJ958648	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon rePAT5_deg,
			partial sequence
R2	KJ958647	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon rePAT4_deg,
			partial sequence
R2	KJ958646	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon rePAT3_deg,
			partial sequence
R2	KJ958645	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon rePAT2_deg,
			partial sequence
R2	KJ958644	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon rePAT1_deg,
			partial sequence
R2	KJ958643	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon rePAT9_deg,
			partial sequence
R2	KJ958642	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon trKOR2_deg,
			partial sequence
R2	KJ958641	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reGAB9_deg,
			partial sequence
R2	KJ958640	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reGAB8_deg,
			partial sequence
R2	KJ958639	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reGAB7_deg,
			partial sequence
R2	KJ958638	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reGAB6_deg,
			partial sequence
R2	KJ958637	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reGAB5_deg,
			partial sequence
R2	KJ958636	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reGAB4_deg,
			partial sequence
R2	KJ958635	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reGAB3_deg,
			partial sequence
R2	KJ958634	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reGAB2_deg,
			partial sequence
R2	KJ958633	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reGAB1_deg,
			partial sequence
R2	KJ958632	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS1_deg,
			partial sequence
R2	KJ958631	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS11_deg,
			partial sequence
R2	KJ958629	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCOM8,
			partial sequence
R2	KJ958628	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCOM6,
			partial sequence
R2	KJ958627	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCOM4,
			partial sequence
R2	KJ958626	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCOM1,
			partial sequence
R2	KJ958624	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon trKOR10,
			partial sequence
R2	KJ958623	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reGAB10,
			partial sequence
R2	KJ958619	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon trKOR4,
			partial sequence
R2	KJ958618	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon trKOR3,
			partial sequence
R2	KJ958617	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon trKOR1,
			partial sequence
R2	KJ958613	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reVIR4,
			partial sequence
R2	KJ958612	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reVIR3,
			partial sequence
R2	KJ958611	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reVIR2,
			partial sequence
R2	KJ958610	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reVIR1,
			partial sequence
R2	KJ958609	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS17,
			partial sequence
R2	KJ958608	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS16,
			partial sequence
R2	KJ958607	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS15,
			partial sequence
R2	KJ958606	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS14,
			partial sequence
R2	KJ958605	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS13,
			partial sequence
R2	KJ958604	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS12,
			partial sequence
R2	KJ958603	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS7,
			partial sequence
R2	KJ958602	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS6,
			partial sequence
R2	KJ958601	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS5,
			partial sequence
R2	KJ958600	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS4,
			partial sequence
R2	KJ958599	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS3,
			partial sequence
R2	KJ958598	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reTDS2,
			partial sequence
R2	KJ958594	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reBER4,
			partial sequence
R2	KJ958593	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reBER2,
			partial sequence
R2	KJ958592	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reBER1,
			partial sequence
R2	KJ958591	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roFOL7,
			partial sequence
R2	KJ958590	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roFOL6,
			partial sequence
R2	KJ958589	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roFOL5,
			partial sequence
R2	KJ958588	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roFOL4,
			partial sequence
R2	KJ958587	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roFOL3,
			partial sequence
R2	KJ958586	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roFOL2,
			partial sequence
R2	KJ958585	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roFOL1,
			partial sequence
R2	KJ958584	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roANZ10,
			partial sequence
R2	KJ958583	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roANZ9,
			partial sequence
R2	KJ958582	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roANZ8,
			partial sequence
R2	KJ958581	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roANZ7,
			partial sequence
R2	KJ958580	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roANZ6,
			partial sequence
R2	KJ958579	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roANZ5,
			partial sequence
R2	KJ958578	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roANZ4,
			partial sequence
R2	KJ958577	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roANZ3,
			partial sequence
R2	KJ958576	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roANZ2,
			partial sequence
R2	KJ958575	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roANZ1,
			partial sequence
R2	KJ958574	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roCAP9,
			partial sequence
R2	KJ958573	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roCAP8,
			partial sequence
R2	KJ958572	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roCAP7,
			partial sequence
R2	KJ958571	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roCAP6,
			partial sequence
R2	KJ958570	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roCAP5,
			partial sequence
R2	KJ958569	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roCAP4,
			partial sequence
R2	KJ958568	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roCAP3,
			partial sequence
R2	KJ958567	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roCAP2,
			partial sequence
R2	KJ958566	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roCAP1,
			partial sequence
R2	KJ958565	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon roCAP10,
			partial sequence
R2	JN937654	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate lu8a 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937653	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate lu7a 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937652	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate lu2a 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937651	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate b7c7 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937650	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate b6c4 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937649	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate lu5a 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937648	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate lu1a 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937647	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate b6c5 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937646	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate b6c6 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937645	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate lu4a 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937644	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate lu3a 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937643	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate b6c3 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937642	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate lu6a 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			psR2Ll, complete sequence
R2	JN937641	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate LM5h2 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			R2Ll, complete sequence
R2	JN937640	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate LM2h5 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			R2Ll, complete sequence
R2	JN937639	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate LM2h4 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			R2Ll, complete sequence
R2	JN937638	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate LM5h5 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			R2Ll, complete sequence
R2	JN937637	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate LM5h4 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			R2Ll, complete sequence
R2	JN937636	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate LM5h3 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			R2Ll, complete sequence
R2	JN937635	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate LM5h1 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			R2Ll, complete sequence
R2	JN937634	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate LM2h3 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			R2Ll, complete sequence
R2	JN937633	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate LM2h2 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			R2Ll, complete sequence
R2	JN937632	R2	Lepidurus apus lubbocki	Lepidurus apus
			isolate LM2h1 28S ribosomal	lubbocki
			RNA gene, partial sequence;
			and non-LTR retrotransposon
			R2Ll, complete sequence
R2	JN937631	R2	Lepidurus arcticus isolate	Lepidurus arcticus
			T6 28S ribosomal RNA gene,
			partial sequence; and
			non-LTR retrotransposon
			R2La, complete sequence
R2	JN937630	R2	Lepidurus arcticus isolate	Lepidurus arcticus
			T5 28S ribosomal RNA gene,
			partial sequence; and
			non-LTR retrotransposon
			R2La, complete sequence
R2	JN937629	R2	Lepidurus arcticus isolate	Lepidurus arcticus
			T4 28S ribosomal RNA gene,
			partial sequence; and
			non-LTR retrotransposon
			R2La, complete sequence
R2	JN937628	R2	Lepidurus arcticus isolate	Lepidurus arcticus
			T3 28S ribosomal RNA gene,
			partial sequence; and
			non-LTR retrotransposon
			R2La, complete sequence
R2	JN937627	R2	Lepidurus arcticus isolate	Lepidurus arcticus
			T2 28S ribosomal RNA gene,
			partial sequence; and
			non-LTR retrotransposon
			R2La, complete sequence
R2	JN937626	R2	Lepidurus arcticus isolate	Lepidurus arcticus
			T1 28S ribosomal RNA gene,
			partial sequence; and
			non-LTR retrotransposon
			R2La, complete sequence
R2	JN937625	R2	Lepidurus arcticus isolate	Lepidurus arcticus
			V4 28S ribosomal RNA gene,
			partial sequence; and
			non-LTR retrotransposon
			R2La, complete sequence
R2	JN937624	R2	Lepidurus arcticus isolate	Lepidurus arcticus
			V3 28S ribosomal RNA gene,
			partial sequence; and
			non-LTR retrotransposon
			R2La, complete sequence
R2	JN937623	R2	Lepidurus arcticus isolate	Lepidurus arcticus
			V2 28S ribosomal RNA gene,
			partial sequence; and
			non-LTR retrotransposon
			R2La, complete sequence
R2	JN937622	R2	Lepidurus arcticus isolate	Lepidurus arcticus
			V1 28S ribosomal RNA gene,
			partial sequence; and
			non-LTR retrotransposon
			R2La, complete sequence
R2	JN937615	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3a7f 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937614	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3a5f 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937613	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3a4f 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937612	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3a3f 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937611	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3a2f 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937610	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3_8 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937609	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3_7 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937608	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3_6 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937607	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3_5 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937606	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3_4 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937605	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3_3 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937604	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3_2 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937603	R2	Lepidurus couesii isolate	Lepidurus couesii
			D3_1 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcB, complete sequence
R2	JN937602	R2	Lepidurus couesii isolate	Lepidurus couesii
			C2_5 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcA, complete sequence
R2	JN937601	R2	Lepidurus couesii isolate	Lepidurus couesii
			LcoC2r1_5 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcA, complete sequence
R2	JN937600	R2	Lepidurus couesii isolate	Lepidurus couesii
			LcoC2r1_6 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcA, complete sequence
R2	JN937599	R2	Lepidurus couesii isolate	Lepidurus couesii
			C2_8 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcA, complete sequence
R2	JN937598	R2	Lepidurus couesii isolate	Lepidurus couesii
			C2_4 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcA, complete sequence
R2	JN937597	R2	Lepidurus couesii isolate	Lepidurus couesii
			C2_9 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcA, complete sequence
R2	JN937596	R2	Lepidurus couesii isolate	Lepidurus couesii
			C2_7 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcA, complete sequence
R2	JN937595	R2	Lepidurus couesii isolate	Lepidurus couesii
			C2_6 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcA, complete sequence
R2	JN937594	R2	Lepidurus couesii isolate	Lepidurus couesii
			C2_3 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcA, complete sequence
R2	JN937593	R2	Lepidurus couesii isolate	Lepidurus couesii
			C2_2 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcA, complete sequence
R2	JN937592	R2	Lepidurus couesii isolate	Lepidurus couesii
			C2_1 28S ribosomal RNA
			gene, partial sequence; and
			non-LTR retrotransposon
			R2LcA, complete sequence
R2	AF015822	R2 ORF	Tenebrio molitor	Tenebrio molitor
			retrotransposon R2 reverse
			transcriptase gene, partial cds
R2	AF015817	R2 ORF	Tenebrio molitor	Tenebrio molitor
			retrotransposon R2 reverse
			transcriptase gene, partial cds
R2	AF015816	R2 ORF	Hippodamia convergens	Hippodamia
			retrotransposon R2 reverse	convergens
			transcriptase gene, partial cds
R2	KP657866	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−714).5 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657865	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−714).4 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657863	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−714).2 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657862	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−714).1 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657861	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1297).9 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657860	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1297).8 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657859	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1297).7 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657858	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1297).6 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657857	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1297).5 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657856	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1297).4 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657855	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1297).3 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657854	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1297).2 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657853	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1297).10 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657852	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1297).1 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657851	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1172).9 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657850	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1172).8 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657849	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1172).7 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657848	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1172).6 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657847	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1172).5 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657846	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1172).4 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657845	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1172).3 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657844	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1172).2 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657843	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1172).10 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657842	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roCAP(−1172).1 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657824	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roANZ(−1062).5 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657823	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roANZ(−1062).4 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657822	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roANZ(−1062).3 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657820	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roANZ(−1062).2 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657816	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roANZ(−1062).16 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657814	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roANZ(−1062).14 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657810	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roANZ(−1062).10 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657809	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	roANZ(−1062).1 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657759	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	rePAT(−1297).8 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657757	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	rePAT(−1297).6 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	KP657751	retrotransposon:	Bacillus rossius isolate	Bacillus rossius
		R2Br	rePAT(−1297).1 retrotransposon
			R2Br reverse transcriptase
			gene, partial cds
R2	AB097125	rt	Ciona savignyi	Ciona savignyi
			retrotransposon R2Cs-D DNA,
			partial sequence
R2	AB097124	rt	Ciona intestinalis	Ciona intestinalis
			retrotransposon R2Ci-D DNA,
			partial sequence
R2	AB097123	rt	Ciona intestinalis	Ciona intestinalis
			retrotransposon R2Ci-C DNA,
			partial sequence
R2	AB097121	rt	Ciona intestinalis	Ciona intestinalis
			retrotransposon R2Ci-A DNA,
			complete sequence
R2	AB201417	rt	Triops longicaudatus non-LTR	Triops
			retrotransposon R2Tl gene	longicaudatus
			for reverse transcriptase,
			partial cds
R2	AB201416	rt	Procambarus clarkii non-LTR	Procambarus
			retrotransposon R2Pc gene for	clarkii
			reverse transcriptase,
			partial cds
R2	AB201415	rt	Hasarius adansoni non-LTR	Hasarius adansoni
			retrotransposon R2Ha gene for
			reverse transcriptase,
			partial cds
R2	AB201414	rt	Metacrinus rotundus non-LTR	Metacrinus
			retrotransposon R2Mr gene for	rotundus
			reverse transcriptase,
			partial cds
R2	AB201413	rt	Mauremys reevesii non-LTR	Mauremys reevesii
			retrotransposon R2Cr-B2 gene
			for reverse transcriptase,
			partial cds
R2	AB201412	rt	Mauremys reevesii non-LTR	Mauremys reevesii
			retrotransposon R2Cr-B1 gene
			for reverse transcriptase,
			partial cds
R2	AB201411	rt	Mauremys reevesii non-LTR	Mauremys reevesii
			retrotransposon R2Cr-A gene
			for reverse transcriptase,
			partial cds
R2	AB201410	rt	Oryzias latipes non-LTR	Oryzias latipes
			retrotransposon R2Ol-A gene
			for reverse transcriptase,
			partial cds
R2	AB201409	rt	Tanichthys albonubes non-LTR	Tanichthys
			retrotransposon R2Ta gene	albonubes
			for reverse transcriptase,
			partial cds
R2	AB201408	rt	Eptatretus burgeri non-LTR	Eptatretus
			retrotransposon R2Eb gene for	burgeri
			reverse transcriptase,
			partial cds
R2	DQ099732	transposon:	Aedes aegypti transposon R2-	Aedes aegypti
		R2-like	like non-LTR retrotransposon
		non-LTR	R2Ag reverse transcriptase
		retrotransposon	(pol) gene, partial cds
		R2Ag
R2	DQ099728	transposon:	Aedes aegypti transposon R2-	Aedes aegypti
		R2-like	like non-LTR retrotransposon
		non-LTR	R2Ag_B reverse transcriptase
		retrotransposon	(pol) gene, partial cds
		R2Ag_B
R2	GU949559		Kalotermes flavicollis	Kalotermes
			isolate Livorno non-LTR	flavicollis
			retrotransposon R2, complete
			sequence; and R2 protein
			gene, complete cds
R2	GU949557		Reticulitermes balkanensis	Reticulitermes
			non-LTR retrotransposon R2,	balkanensis
			partial sequence; and R2
			protein gene, partial cds
R2	GU949556		Reticulitermes grassei	Reticulitermes
			non-LTR retrotransposon R2,	grassei
			partial sequence; and R2
			protein gene, partial cds
R2	GU949554		Reticulitermes urbis non-LTR	Reticulitermes
			retrotransposon R2, complete	urbis
			sequence; and R2 protein
			gene, complete cds
R2	AF412214		Schistosoma japonicum clone	Schistosoma
			S10A non-LTR retrotransposon	japonicum
			SjR2-like, partial sequence
R2	AF015685		Drosophila mercatorum R2	Drosophila
			retrotransposon reverse	mercatorum
			transcriptase domain protein
			gene, complete cds
R2	KJ958674		Bacillus rossius	Bacillus rossius
			retrotransposon R2Br,
			complete sequence
R2	AF015814	R2	Limulus polyphemus	Limulus polyphemus
			retrotransposon R2, complete
			sequence
R2	M16558	R2	Bombyx mori rDNA insertion	Bombyx mori
			element R2 (typeII), complete
			cds.
R2	GQ398057	R9Av	Adineta vaga copy 1 non-LTR	Adineta vaga
			retrotransposon R9, complete
			sequence; and disrupted 28S
			ribosomal RNA gene, partial
			sequence
R2Bm	AB076841	R2	Bombyx mori non-LTR	Bombyx mori
			retrotransposon R2Bm gene
			for reverse transcriptase,
			complete cds and 28S rRNA
R2Ci-B	AB097122	rt	Ciona intestinalis	Ciona intestinalis
			retrotransposon R2Ci-B DNA,
			complete sequence
R2Dr	AB097126	rt	Danio rerio retrotransposon	Danio rerio
			R2Dr DNA, complete sequence
R4	AH003588		Parascaris equorum transposon	Parascaris equorum
			non-LTR retrotransposable
			element R4 reverse
			transcriptase gene, partial cds
R4	ALU29445	R4	Ascaris lumbricoides	Ascaris
			site-specific non-LTR	lumbricoides
			retrotransposable element
			R4 in 26S rDNA, complete
			sequence
R4	L08889	R4 Dong	Bombyx mori reverse	Bombyx mori
			transcriptase gene, complete cds
R4	DQ836390	MalR4-5	Maculinea alcon R4-like	Phengaris alcon
			non-LTR retrotransposon R4-5
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836385	MnaR4-3	Maculinea nausithous R4-like	Phengaris
			non-LTR retrotransposon R4-3	nausithous
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836386	MnaR4-4	Maculinea nausithous R4-like	Phengaris
			non-LTR retrotransposon R4-4	nausithous
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836387	MnaR4-7	Maculinea nausithous R4-like	Phengaris
			non-LTR retrotransposon R4-7	nausithous
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836388	MnaR4-8	Maculinea nausithous R4-like	Phengaris
			non-LTR retrotransposon R4-8	nausithous
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836389	MnaR4-9	Maculinea nausithous R4-like	Phengaris
			non-LTR retrotransposon R4-9	nausithous
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836379	MteR4-1	Maculinea teleius R4-like	Phengaris teleius
			non-LTR retrotransposon R4-1
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836384	MteR4-10	Maculinea teleius R4-like	Phengaris teleius
			non-LTR retrotransposon R4-10
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836367	MteR4-2	Maculinea teleius R4-like	Phengaris teleius
			non-LTR retrotransposon R4-2
			reverse transcriptase (RT)
			gene, partial cds
R4	DQ836380	MteR4-3	Maculinea teleius R4-like	Phengaris teleius
			non-LTR retrotransposon R4-3
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836381	MteR4-4	Maculinea teleius R4-like	Phengaris teleius
			non-LTR retrotransposon R4-4
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836382	MteR4-6	Maculinea teleius R4-like	Phengaris teleius
			non-LTR retrotransposon R4-6
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836383	MteR4-8	Maculinea teleius R4-like	Phengaris teleius
			non-LTR retrotransposon R4-8
			reverse transcriptase (RT)
			pseudogene, partial sequence
R4	DQ836374	transposon:	Maculinea alcon R4-like	Phengaris alcon
		R4-like	non-LTR retrotransposon R4-1
		non-LTR	reverse transcriptase (RT)
		retrotransposon	gene, partial cds
		R4-1
R4	DQ836373	transposon:	Maculinea nausithous R4-like	Phengaris
		R4-like	non-LTR retrotransposon R4-1	nausithous
		non-LTR	reverse transcriptase (RT)
		retrotransposon	gene, partial cds
		R4-1
R4	DQ836375	transposon:	Maculinea alcon R4-like	Phengaris alcon
		R4-like	non-LTR retrotransposon R4-2
		non-LTR	reverse transcriptase (RT)
		retrotransposon	gene, partial cds
		R4-2
R4	DQ836376	transposon:	Maculinea alcon R4-like	Phengaris alcon
		R4-like	non-LTR retrotransposon R4-3
		non-LTR	reverse transcriptase (RT)
		retrotransposon	gene, partial cds
		R4-3
R4	DQ836377	transposon:	Maculinea alcon R4-like	Phengaris alcon
		R4-like	non-LTR retrotransposon R4-4
		non-LTR	reverse transcriptase (RT)
		retrotransposon	gene, partial cds
		R4-4
R4	DQ836371	transposon:	Maculinea nausithous R4-like	Phengaris
		R4-like	non-LTR retrotransposon R4-5	nausithous
		non-LTR	reverse transcriptase (RT)
		retrotransposon	gene, partial cds
		R4-5
R4	DQ836368	transposon:	Maculinea teleius R4-like	Phengaris teleius
		R4-like	non-LTR retrotransposon R4-5
		non-LTR	reverse transcriptase (RT)
		retrotransposon	gene, partial cds
		R4-5
R4	DQ836378	transposon:	Maculinea alcon R4-like	Phengaris alcon
		R4-like	non-LTR retrotransposon R4-6
		non-LTR	reverse transcriptase (RT)
		retrotransposon	gene, partial cds
		R4-6
R4	DQ836372	transposon:	Maculinea nausithous R4-like	Phengaris
		R4-like	non-LTR retrotransposon R4-6	nausithous
		non-LTR	reverse transcriptase (RT)
		retrotransposon	gene, partial cds
		R4-6
R4	DQ836369	transposon:	Maculinea teleius R4-like	Phengaris teleius
		R4-like	non-LTR retrotransposon R4-7
		non-LTR	reverse transcriptase (RT)
		retrotransposon	gene, partial cds
		R4-7
R4	DQ836370	transposon:	Maculinea teleius R4-like	Phengaris teleius
		R4-like	non-LTR retrotransposon R4-9
		non-LTR	reverse transcriptase (RT)
		retrotransposon	gene, partial cds
		R4-9
R4	AF286191	transposon:	Xiphophorus maculatus	Xiphophorus
		retrotransposon	retrotransposon Rex6 reverse	maculatus
		Rex6	transcriptase pseudogene,
			partial sequence
R5	KJ958673	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reCUR5_deg,
			partial sequence
R5	KJ958620	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon trKOR5,
			partial sequence
R5	KJ958614	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reVIR5,
			partial sequence
R5	KJ958595	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reBER5,
			partial sequence
R5	AJ006560	transposon:	Anopheles merus Amer5 non-LTR	Anopheles merus
		Amer5	retrotransposon encoding
		non-LTR	reverse transcriptase, partial
		retrotransposon
R5	AF352479	transposon:	Chironomus circumdatus clone	Chironomus
		NLRCth1-like	cir5 transposon NLRCth1-like	circumdatus
		non-LTR	non-LTR retrotransposon
		retrotransposon	reverse transcriptase gene,
			partial cds
R5	AF352454	transposon:	Chironomus alpestris clone	Chironomus
		NLRCth1-like	dor50 transposon NLRCth1-like	alpestris
		non-LTR	non-LTR retrotransposon
		retrotransposon	reverse transcriptase gene,
			partial cds
R5	AF352404	transposon:	Chironomus luridus clone lur5	Chironomus luridus
		NLRCth1-like	transposon NLRCth1-like
		non-LTR	non-LTR retrotransposon
		retrotransposon	reverse transcriptase gene,
			partial cds
R8	FR852798	poly(A) tail	Beta vulgaris subsp.	Beta vulgaris
			vulgaris	subsp. vulgaris
			LINE-type retrotransposon
			Belline2_3
R8	KJ958630	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon reVIR8_deg,
			partial sequence
R8	KJ958621	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon trKOR8,
			partial sequence
R8	KP001560	rex3-RT	Iberochondrostoma lusitanicum	Iberochondrostoma
		pseudogene_Contig	clone tr8a non-LTR	lusitanicum
		ILU_TR8	retrotransposon Rex3,
			complete sequence
R8	FR852885	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgaris	subsp. vulgaris
			LINE-type retrotransposon
			BNR114 (Belline1_114)
R8	FR852856	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			BNR45 (Belline1_45)
R8	FR852844	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			BNR22 (Belline1_22)
R8	FR852836	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			Belline17_6
R8	FR852834	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			Belline17_4
R8	FR852831	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			Belline17_1
R8	FR852829	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			Belline16_2
R8	FR852827	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			Belline15_3
R8	FR852819	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			Belline12_2
R8	FR852813	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			Belline9_5
R8	FR852807	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			Belline8_1
R8	FR852806	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			Belline7_18
R8	FR852799	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			Belline2_4
R8	FR852795	right terminal	Beta vulgaris subsp.	Beta vulgaris
		repeat	vulgarius	subsp. vulgaris
			LINE-type retrotransposon
			BNR19 (Belline1_19)
R8	AF352481	transposon:	Chironomus circumdatus clone	Chironomus
		NLRCth1-like	cir8 transposon NLRCth1-like	circumdatus
		non-LTR	non-LTR retrotransposon
		retrotransposon	reverse transcriptase gene,
			partial cds
R8;	FR852861	right terminal	Beta vulgaris subsp.	Beta vulgaris
R5		repeat	vulgaris	subsp. vulgaris
			LINE-type retrotransposon
			BNR59 (Belline1_59)
R8;	FR852857	right terminal	Beta vulgaris subsp.	Beta vulgaris
R5		repeat	vulgaris	subsp. vulgaris
			LINE-type retrotransposon
			BNR51 (Belline1_51)
R8;	FR852866	right terminal	Beta vulgaris subsp.	Beta vulgaris
R7		repeat	vulgaris	subsp. vulgaris
			LINE-type retrotransposon
			BNR76 (Belline1_76)
R8;	FR852838	right terminal	Beta vulgaris subsp.	Beta vulgaris
R7		repeat	vulgaris	subsp. vulgaris
			LINE-type retrotransposon
			BNR7 (Belline1_7)
R8;	AF352455	transposon:	Chironomus alpestris clone	Chironomus
R7		NLRCth1-like	dor70 note identical sequence	alpestris
		non-LTR	found in dor80 transposon
		retrotransposon	NLRCth1-like non-LTR
			retrotransposon reverse
			transcriptase gene, partial cds
R8;	FR852878	right terminal	Beta vulgaris subsp.	Beta vulgaris
R9		repeat	vulgaris	subsp. vulgaris
			LINE-type retrotransposon
			BNR96 (Belline1_96)
R9	KJ958625	R2	Bacillus rossius non-LTR	Bacillus rossius
			retrotransposon trKOR9,
			partial sequence
Rex6	AJ293547	en	Oreochromis niloticus Rex6	Oreochromis
			retrotransposon partial en	niloticus
			pseudogene for endonuclease,
			clone rex6-Oni-3
Rex6	AJ293546	en	Oreochromis niloticus Rex6	Oreochromis
			retrotransposon partial en	niloticus
			pseudogene for endonuclease,
			clone rex6-Oni-2
Rex6	AJ293545	en	Oreochromis niloticus Rex6	Oreochromis
			retrotransposon partial en	niloticus
			pseudogene for endonuclease,
			clone rex6-Oni-1
Rex6	AJ293517	en	Xiphophorus maculatus Rex6	Xiphophorus
			retrotransposon partial en	maculatus
			pseudogene for endonuclease,
			clone Rex6-Xma-6
Rex6	AJ293516	en	Xiphophorus maculatus Rex6	Xiphophorus
			retrotransposon partial en	maculatus
			pseudogene for endonuclease,
			clone Rex6-Xma-5
Rex6	AJ293515	en	Xiphophorus maculatus Rex6	Xiphophorus
			retrotransposon partial en	maculatus
			pseudogene for endonuclease,
			clone Rex6-Xma-4
Rex6	AJ293514	en	Xiphophorus maculatus Rex6	Xiphophorus
			retrotransposon partial en	maculatus
			pseudogene for endonuclease,
			clone Rex6-Xma-3
Rex6	AJ293513	en	Xiphophorus maculatus Rex6	Xiphophorus
			retrotransposon partial en	maculatus
			pseudogene for endonuclease,
			clone Rex6-Xma-2
Rex6	AJ293512	en	Xiphophorus maculatus Rex6	Xiphophorus
			retrotransposon partial en	maculatus
			pseudogene for endonuclease,
			clone Rex6-Xma-1
Rex6	AJ293538	en	Poecilia formosa Rex6	Poecilia formosa
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Pfo-6
Rex6	AJ293537	en	Poecilia formosa Rex6	Poecilia formosa
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Pfo-5
Rex6	AJ293536	en	Poecilia formosa Rex6	Poecilia formosa
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Pfo-4
Rex6	AJ293535	en	Poecilia formosa Rex6	Poecilia formosa
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Pfo-3
Rex6	AJ293534	en	Poecilia formosa Rex6	Poecilia formosa
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Pfo-2
Rex6	AJ293533	en	Poecilia formosa Rex6	Poecilia formosa
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Pfo-1
Rex6	AJ293526	en	Poeciliopsis gracilis Rex6	Poeciliopsis
			retrotransposon partial en	gracilis
			pseudogene for endonuclease,
			clone rex6-Pgr-4
Rex6	AJ293525	en	Poeciliopsis gracilis Rex6	Poeciliopsis
			retrotransposon partial en	gracilis
			pseudogene for endonuclease,
			clone rex6-Pgr-3
Rex6	AJ293524	en	Poeciliopsis gracilis Rex6	Poeciliopsis
			retrotransposon partial en	gracilis
			pseudogene for endonuclease,
			clone rex6-Pgr-2
Rex6	AJ293523	en	Poeciliopsis gracilis Rex6	Poeciliopsis
			retrotransposon partial en	gracilis
			pseudogene for endonuclease,
			clone rex6-Pgr-1
Rex6	AJ293522	en	Oryzias latipes Rex6	Oryzias latipes
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Ola-5
Rex6	AJ293521	en	Oryzias latipes Rex6	Oryzias latipes
			retrotransposon partial en
			pseudogene for endonuclease,
			clone Rex6-Ola-4
Rex6	AJ293520	en	Oryzias latipes Rex6	Oryzias latipes
			retrotransposon partial en
			pseudogene for endonuclease,
			clone Rex6-Ola-3
Rex6	AJ293519	en	Oryzias latipes Rex6	Oryzias latipes
			retrotransposon partial en
			pseudogene for endonuclease,
			clone Rex6-Ola-2
Rex6	AJ293518	en	Oryzias latipes Rex6	Oryzias latipes
			retrotransposon partial en
			pseudogene for endonuclease,
			clone Rex6-Ola-1
Rex6	AJ293549	en	Cichlasoma labridens Rex6	Herichthys
			retrotransposon partial en	labridens
			pseudogene for endonuclease,
			clone rex6-Cla-2
Rex6	AJ293548	en	Cichlasoma labridens Rex6	Herichthys
			retrotransposon partial en	labridens
			pseudogene for endonuclease,
			clone rex6-Cla-1
Rex6	AJ293544	en	Heterandria bimaculata Rex6	Pseudoxiphophorus
			retrotransposon partial en	bimaculatus
			pseudogene for endonuclease,
			clone rex6-Hbi-6
Rex6	AJ293543	en	Heterandria bimaculata Rex6	Pseudoxiphophorus
			retrotransposon partial en	bimaculatus
			pseudogene for endonuclease,
			clone rex6-Hbi-5
Rex6	AJ293542	en	Heterandria bimaculata Rex6	Pseudoxiphophorus
			retrotransposon partial en	bimaculatus
			pseudogene for endonuclease,
			clone rex6-Hbi-4
Rex6	AJ293541	en	Heterandria bimaculata Rex6	Pseudoxiphophorus
			retrotransposon partial en	bimaculatus
			pseudogene for endonuclease,
			clone rex6-Hbi-3
Rex6	AJ293540	en	Heterandria bimaculata Rex6	Pseudoxiphophorus
			retrotransposon partial en	bimaculatus
			pseudogene for endonuclease,
			clone rex6-Hbi-2
Rex6	AJ293539	en	Heterandria bimaculata Rex6	Pseudoxiphophorus
			retrotransposon partial en	bimaculatus
			pseudogene for endonuclease,
			clone rex6-Hbi-1
Rex6	AJ293532	en	Gambusia affinis Rex6	Gambusia affinis
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Gaf-5
Rex6	AJ293531	en	Gambusia affinis Rex6	Gambusia affinis
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Gaf-5
Rex6	AJ293530	en	Gambusia affinis Rex6	Gambusia affinis
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Gaf-4
Rex6	AJ293529	en	Gambusia affinis Rex6	Gambusia affinis
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Gaf-3
Rex6	AJ293528	en	Gambusia affinis Rex6	Gambusia affinis
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Gaf-2
Rex6	AJ293527	en	Gambusia affinis Rex6	Gambusia affinis
			retrotransposon partial en
			pseudogene for endonuclease,
			clone rex6-Gaf-1
Rex6	JX576459	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	i non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576458	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	h non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576457	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	g non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576456	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	f non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576455	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	e non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576454	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	d non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576453	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	c non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576452	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	b non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576451	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	a non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576450	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	z8 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576449	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	z7 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576448	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	z6 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576447	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	z5 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576446	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	z4 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576445	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	z3 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576444	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	z2 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576443	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	z1 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576442	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	z non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576441	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	x non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576440	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	v non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576439	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	u non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576438	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	t non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576437	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	s non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576436	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	r non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576435	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	q non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576434	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	p non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576433	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	o non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576432	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	n non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576431	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	m non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576430	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	l non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576429	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	k non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576428	non-LTR	Symphysodon discus isolate	Symphysodon discus
		retrotransposon:	j non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576427	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	e non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	JX576426	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	d non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	JX576425	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	c non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	JX576424	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	b non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	JX576423	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	a non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	JX576422	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	g non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576421	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	f non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576420	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	e non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576419	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	d non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576418	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	c non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576417	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	b non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576416	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	a non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576415	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	g non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	JX576414	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	f non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	JX576413	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	e non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	JX576412	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	d non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	JX576411	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	c non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	JX576410	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	b non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	JX576409	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	a non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	JX576408	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	h non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576407	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	g non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576406	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	f non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576405	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	e non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576404	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	d non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576403	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	c non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576402	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	b non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	JX576401	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	a non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131853	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	z7 non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131852	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	z6 non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131851	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	z5 non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131850	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	z4 non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131849	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	z3 non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131848	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	z2 non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131847	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	z1 non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131846	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	z non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131845	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	x non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131844	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	v non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131843	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	u non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131842	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	t non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131841	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	s non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131840	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	r non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131839	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	q non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131838	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	p non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131837	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	n non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131836	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	m non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131835	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	l non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131834	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	k non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131833	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	j non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131832	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	i non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131831	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	h non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131830	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	g non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131829	non-LTR	Pterophyllum scalare clone	Pterophyllum
		retrotransposon:	f non-LTR retrotransposon	scalare
		Rex6	Rex6, partial sequence
Rex6	KF131828	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	z6 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131827	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	z5 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131826	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	z4 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131825	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	z3 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131824	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	z2 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131823	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	z1 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131822	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	z non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131821	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	x non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131820	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	v non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131819	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	u non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131818	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	t non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131817	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	s non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131816	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	r non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131815	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	q non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131814	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	p non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131813	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	o non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131812	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	n non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131811	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	m non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131810	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	l non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131809	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	k non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131808	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	j non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131807	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	i non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131806	non-LTR	Geophagus proximus clone	Geophagus proximus
		retrotransposon:	h non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131805	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	z10 non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131804	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	z9 non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131803	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	z8 non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131802	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	z7 non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131801	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	z6 non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131800	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	z5 non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131799	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	z4 non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131798	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	z3 non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131797	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	z2 non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131796	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	z1 non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131795	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	z non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131794	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	x non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131793	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	v non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131792	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	u non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131791	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	t non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131790	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	s non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131789	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	r non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131788	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	q non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131787	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	p non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131786	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	o non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131785	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	n non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131784	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	m non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131783	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	l non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131782	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	k non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131781	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	j non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131780	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	i non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131779	non-LTR	Astronotus ocellatus clone	Astronotus
		retrotransposon:	h non-LTR retrotransposon	ocellatus
		Rex6	Rex6, partial sequence
Rex6	KF131778	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	z6 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131777	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	z5 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131776	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	z4 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131775	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	z3 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131774	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	z2 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131773	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	z1 non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131772	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	z non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131771	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	x non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131770	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	v non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131769	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	u non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131768	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	t non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131767	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	s non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131766	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	r non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131765	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	q non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131764	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	p non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131763	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	o non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131762	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	n non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131761	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	m non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131760	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	l non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131759	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	k non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131758	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	j non-LTR retrotransposon
		Rex6	Rex6, partial sequence
Rex6	KF131757	non-LTR	Cichla monoculus clone	Cichla monoculus
		retrotransposon:	i non-LTR retrotransposon
		Rex6	Rex6, partial sequence
SLACS	JN608782	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-46 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608781	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-45 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608780	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-41 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608779	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-40 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608778	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-38 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608777	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-37 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608776	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-36 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608775	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-35 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608774	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-34 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608773	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-33 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608772	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-32 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608771	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-30 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608770	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-29 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608769	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-28 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608768	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-27 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608767	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-26 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608766	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-25 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608765	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-24 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608764	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-23 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608763	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-22 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608762	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-20 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608761	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-19 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608760	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-18 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608759	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-17 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608758	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-16 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608757	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-13 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608756	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-12 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608755	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-11 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608754	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-10 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608753	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-08 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608752	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-07 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608751	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-06 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608750	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-05 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608749	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-04 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608748	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-03 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608747	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	Y-01 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608746	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-83 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608745	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-81 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608744	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-80 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608743	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-79 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608742	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-78 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608741	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-76 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608740	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-75 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608739	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-74 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608738	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-66 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608737	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-65 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608736	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-62 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608735	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-61 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608734	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-60 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608733	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-59 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608732	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-57 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608731	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-49 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608730	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-41 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608729	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-28 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608728	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-27 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608727	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-23 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608726	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-21 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608725	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-14 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608724	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-11 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608723	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-07 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608722	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-06 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608721	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-05 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608720	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-03 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608719	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	X-01 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608718	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG40 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608717	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG39 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608716	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG38 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608715	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG37 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608714	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG36 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608713	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG35 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608712	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG34 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608711	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG33 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608710	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG32 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608709	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG31 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608708	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG30 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608707	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG29 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608706	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG28 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608705	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG27 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608704	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG26 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608703	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG25 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608702	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG24 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608701	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG23 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608700	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG22 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608699	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG21 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608698	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG20 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608697	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG19 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608696	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG18 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608695	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG17 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608694	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG16 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608693	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG14 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608692	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG13 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608691	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG12 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608690	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG11 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608689	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG10 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608688	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG09 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608687	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG08 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608686	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG07 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608685	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG06 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608684	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG05 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608683	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG04 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608682	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG03 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608681	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG02 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608680	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mG01 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608679	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG40 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608678	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG39 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608677	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG38 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608676	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG37 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608675	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG36 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608674	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG35 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608673	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG34 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608672	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG33 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608671	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG32 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608670	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG31 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608669	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG30 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608668	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG29 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608667	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG28 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608666	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG27 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608665	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG26 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608664	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG25 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608663	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG24 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608662	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG23 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608661	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG22 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608660	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG21 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608659	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG20 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608658	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG19 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608657	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG18 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608656	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG17 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608655	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG16 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608654	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG15 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608653	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG14 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608652	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG13 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608651	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG11 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608650	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG10 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608649	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG09 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608648	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG08 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608647	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG07 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608646	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG06 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608645	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG05 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608644	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG03 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608643	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG02 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608642	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fG01 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608641	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-47 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608640	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-46 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608639	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-45 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608638	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-44 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608637	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-42 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608636	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-41 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608635	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-40 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608634	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-37 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608633	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-36 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608632	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-35 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608631	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-34 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608630	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-33 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608629	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-32 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608628	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-31 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608627	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-26 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608626	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-24 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608625	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-23 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608624	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-22 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608623	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-21 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608622	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-20 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608621	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-19 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608620	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-18 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608619	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-17 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608618	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-16 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608617	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-15 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608616	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-14 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608615	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-13 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608614	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-12 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608613	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-11 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608612	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-10 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608611	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-09 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608610	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-08 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608609	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-06 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608608	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-05 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608607	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-03 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608606	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	A-01 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608236	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR40 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608235	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR39 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608234	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR38 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608233	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR35 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608232	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR32 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608231	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR29 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608230	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR26 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608229	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR25 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608228	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR18 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608227	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR17 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608226	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR14 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608225	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR13 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608224	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR12 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608223	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR11 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608222	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR09 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608221	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR08 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608220	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR07 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608219	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR06 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608218	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR05 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608217	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR04 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608216	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR03 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608215	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR02 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608214	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mR01 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608213	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL40 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608212	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL39 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608211	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL37 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608210	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL36 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608209	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL35 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608208	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL34 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608207	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL33 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608206	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL32 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608205	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL31 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608204	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL28 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608203	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL27 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608202	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL25 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608201	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL24 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608200	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL23 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608199	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL19 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608198	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL16 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608197	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL13 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608196	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL12 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608195	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL11 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608194	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL10 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608193	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL07 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608192	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL04 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608191	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL03 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608190	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL02 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608189	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mL01 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608188	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF40 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608187	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF39 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608186	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF38 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608185	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF37 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608184	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF36 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608183	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF35 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608182	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF33 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608181	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF32 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608180	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF31 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608179	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF30 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608178	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF29 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608177	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF28 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608176	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF27 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608175	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF26 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608174	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF25 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608173	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF23 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608172	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF22 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608171	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF21 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608170	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF20 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608169	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF19 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608168	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF18 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608167	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF17 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608166	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF16 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608165	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF15 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608164	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF14 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608163	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF13 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608162	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF11 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608161	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF10 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608160	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF09 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608159	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF08 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608158	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF07 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608157	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF06 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608156	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF05 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608155	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF04 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608154	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF03 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608153	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF02 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608152	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	mF01 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608151	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR40 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608150	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR39 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608149	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR38 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608148	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR37 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608147	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR36 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608146	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR35 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608145	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR34 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608144	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR33 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608143	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR32 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608142	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR31 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608141	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR30 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608140	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR29 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608139	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR28 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608138	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR27 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608137	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR26 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608136	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR25 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608135	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR24 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608134	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR23 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608133	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR22 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608132	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR21 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608131	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR20 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608130	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR19 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608129	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR18 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608128	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR17 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608127	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR16 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608126	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR15 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608125	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR14 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608124	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR13 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608123	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR12 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608122	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR11 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608121	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR09 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608120	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR08 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608119	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR07 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608118	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR05 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608117	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR04 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608116	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR03 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608115	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR02 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608114	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fR01 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608113	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL40 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608112	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL39 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608111	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL38 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608110	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL37 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608109	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL36 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608108	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL35 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608107	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL34 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608106	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL33 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608105	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL32 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608104	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL31 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608103	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL30 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608102	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL29 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608101	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL28 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608100	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL27 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608099	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL26 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608098	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL25 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608097	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL24 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608096	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL23 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608095	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL22 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608094	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL20 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608093	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL19 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608092	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL18 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608091	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL17 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608090	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL16 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608089	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL15 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608088	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL14 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608087	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL13 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608086	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL12 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608085	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL11 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608084	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL10 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608083	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL09 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608082	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL07 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608081	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL06 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608080	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL05 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608079	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL04 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608078	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL03 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608077	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fL01 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608076	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF40 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608075	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF39 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608074	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF38 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608073	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF37 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608072	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF36 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608071	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF35 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608070	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF34 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608069	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF33 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608068	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF32 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608067	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF31 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608066	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF30 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608065	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF29 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608064	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF28 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608063	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF27 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608062	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF26 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608061	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF24 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608060	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF23 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608059	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF21 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608058	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF20 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608057	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF18 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608056	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF17 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608055	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF16 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608054	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF15 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608053	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF14 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608052	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF13 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608051	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF12 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608050	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF11 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608049	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF10 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608048	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF09 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608047	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF08 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608046	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF06 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608045	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF05 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608044	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF04 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608043	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF03 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
SLACS	JN608042	non-LTR	Silene latifolia isolate	Silene latifolia
		retrotransposon:	fF02 non-LTR retrotransposon
		SLACS-like	SLACS-like, partial sequence
YURECi	AB097133	rt	Ciona intestinalis	Ciona intestinalis
			retrotransposon YURECi DNA,
			complete sequence
CRE	.	Cnl1	C. neoformans non-LTR	Cryptococcus
			retrotransposon - consensus.	neoformans
CRE	.	CRE-1_ACas	CRE non-LTR retrotransposon:	Acanthamoeba
			consensus.	castellanii
CRE	.	Cre-1_BM	Cre-1_BM non-LTR	Bombyx mori
			retrotransposon - consensus.
CRE	.	CRE-1_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	Cre-1_FCy	Cre-1_FCy non-LTR	Fragilariopsis
			retrotransposon - conceptual	cylindrus
			consensus.
CRE	.	Cre-1_HM	Cre-1_HM non-LTR	Hydra vulgaris
			retrotransposon - consensus.
CRE	.	CRE-1_HRo	Cre-like non-LTR	Helobdella robusta
			retrotransposon: consensus
			sequence.
CRE	.	CRE-1_LSa	CRE non-LTR retrotransposon:	Lactuca sativa
			consensus.
CRE	.	Cre-1_MB	Cre-1_MB non-LTR	Monosiga
			retrotransposon - consensus.	brevicollis
CRE	.	Cre-1_NV	Cre-1_NV non-LTR	Nematostella
			retrotransposon - consensus.	vectensis
CRE	.	CRE-1_PXu	Non-LTR retrotransposon from	Papilio xuthus
			Papilio xuthus: consensus.
CRE	.	CRE-10_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-11_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-12_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-13_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-14_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-15_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-16_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-17_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	Cre-2_BM	Cre-2_BM non-LTR	Bombyx mori
			retrotransposon - consensus.
CRE	.	CRE-2_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-2_HMa	CRE non-LTR retrotransposon:	Hydra vulgaris
			consensus.
CRE	.	CRE-2_HRo	Cre-like non-LTR	Helobdella robusta
			retrotransposon: consensus
			sequence.
CRE	.	CRE-2_NV	CRE non-LTR retrotransposon:	Nematostella
			consensus.	vectensis
CRE	.	CRE-2_PXu	Non-LTR retrotransposon from	Papilio xuthus
			Papilio xuthus: consensus.
CRE	.	CRE-3_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-3_HRo	CRE-like non-LTR	Helobdella robusta
			retrotransposon: consensus
			sequence.
CRE	.	CRE-3_NV	CRE non-LTR retrotransposon:	Nematostella
			consensus.	vectensis
CRE	.	CRE-4_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-4_HRo	CRE-like non-LTR	Helobdella robusta
			retrotransposon: consensus
			sequence.
CRE	.	CRE-5_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-5_HRo	CRE-like non-LTR	Helobdella robusta
			retrotransposon: consensus
			sequence.
CRE	.	CRE-6_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-6_HRo	CRE-like non-LTR	Helobdella robusta
			retrotransposon: consensus
			sequence.
CRE	.	CRE-7_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-8_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	.	CRE-9_CCri	Non-LTR retrotransposon from	Chondrus crispus
			the red seaweed: consensus.
CRE	M33009	CRE1	C. fasciculata retrotransposable	Crithidia
			element (CRE1).	fasciculata
CRE	U19151	CRE2	C. fasciculata retrotransposable	Crithidia
			element (CRE2).	fasciculata
CRE	M62862	CZAR	T. cruzi SL-RNA-associated	Trypanosoma cruzi
			non-LTR retrotransposon.
R4	.	Dong	Bombyx mori non-LTR	Bombyx mori
			retrotransposable element.
R4	.	DONG_FR2	Non-LTR retrotransposon;	Takifugu rubripes
			site-specific LINE; R4/Dong
			superfamily; DONG_FR2.
R4	.	Dong-1_AFC	Dong/R4-type non-LTR	Cichlidae
			retrotransposon - consensus.
R4	.	Dong-1_HMM	Non-LTR retrotransposon	Heliconius
			family from Heliconius	melpomene
			melpomene melpomene.	melpomene
R4	.	Dong-1_NVe	A Dong non-LTR	Nematostella
			retrotransposon family from	vectensis
			Nematostella vectensis.
R4	.	Dong-1_PPo	Non-LTR retrotransposon from	Papilio polytes
			Papilio polytes: consensus.
R4	.	Dong-1_PXu	Non-LTR retrotransposon from	Papilio xuthus
			Papilio xuthus: consensus.
R4	.	Dong-2_BM	Non-LTR retrotransposon - a	Bombyx mori
			consensus.
R4	.	Dong-2_HMM	Non-LTR retrotransposon	Heliconius
			family from Heliconius	melpomene
			melpomene melpomene.	melpomene
R4	.	Dong-2_Lch	Dong-like non-LTR	Latimeria
			retrotransposon - consensus.	chalumnae
R4	.	Dong-2_PPo	Non-LTR retrotransposon from	Papilio polytes
			Papilio polytes: consensus.
R4	.	DongAa	A Dong non-LTR	Aedes aegypti
			retrotransposon family from
			Aedes aegypti.
R4	AB097127	DongAG	Anopheles gambiae non-LTR	Anopheles
			retrotransposon DongAg - a	gambiae
			partial sequence.
R4	AB097128	EhRLE2	Entamoeba histolytica	Entamoeba
			retrotransposon EhRLE2,	histolytica
			complete sequence.
R4	AB097129	EhRLE3	Entamoeba histolytica	Entamoeba
			retrotransposon EhRLE3,	histolytica
			complete sequence.
HERO	.	HERO-1_AFC	Hero-type non-LTR	Cichlidae
			retrotransposon - consensus.
HERO	.	HERO-1_BF	Amphioxus HERO-1_BF	Branchiostoma
			autonomous non-LTR	floridae
			Retrotransposon - consensus.
HERO	.	HERO-1_HR	A family of HERO non-LTR	Helobdella robusta
			retrotransposons - a
			consensus sequence.
HERO	.	HERO-1_PP	A family of HERO non-LTR	Physarum
			retrotransposons - a	polycephalm
			consensus sequence.
HERO	AAGJ02121261	HERO-1_SP	Sea urchin HERO-1_SP	Strongylocentrotus
			autonomous non-LTR	purpuratus
			Retrotransposon - consensus.
HERO	.	HERO-2_BF	Amphioxus HERO-2_BF	Branchiostoma
			autonomous non-LTR	floridae
			Retrotransposon - consensus.
HERO	.	HERO-2_DR	HERO-2_DR is a family of HERO	Danio rerio
			non-LTR retrotransposons - a
			consensus.
HERO	.	HERO-2_HR	Non-LTR retrotransposon:	Helobdella robusta
			consensus sequence.
HERO	048B05	Hero-2_SPur	HERO-type non-ltr	Strongylocentrotus
			retrotransposon from sea urchin.	purpuratus
HERO	.	HERO-3_BF	HERO-3_BF is a family of HERO	Branchiostoma
			non-LTR retrotransposons - a	floridae
			consensus.
HERO	.	HERO-3_DR	HERO-3_DR is a family of HERO	Danio rerio
			non-LTR retrotransposons - a
			consensus.
HERO	.	HERO-3_HR	Non-LTR retrotransposon:	Helobdella robusta
			consensus sequence.
HERO	.	Hero-3_SPur	HERO-type non-LTR	Strongylocentrotus
			retrotransposon from sea urchin.	purpuratus
HERO	.	HERO-4_DR	HERO-4_DR is a family of HERO	Danio rerio
			non-LTR retrotransposons - a
			consensus.
HERO	.	HERO-4_HR	Non-LTR retrotransposon:	Helobdella robusta
			consensus sequence.
HERO	.	HERO-5_HR	Non-LTR retrotransposon:	Helobdella robusta
			consensus sequence.
HERO	.	HERO-6_HR	Non-LTR retrotransposon:	Helobdella robusta
			consensus sequence.
HERO	.	HERO-7_HR	Non-LTR retrotransposon:	Helobdella robusta
			consensus sequence.
HERO	.	HERO-8_HR	Non-LTR retrotransposon:	Helobdella robusta
			consensus sequence.
HERO	.	HERO-9_HR	Non-LTR retrotransposon:	Helobdella robusta
			consensus sequence.
HERO	.	HERODr	HERODr is a family of HERO	Danio rerio
			non-LTR retrotransposons - a
			consensus.
HERO	.	HEROFr	A HERO clade non-LTR	Takifugu rubripes
			Retrotransposon family -
			consensus.
HERO	.	HEROTn	HEROTn or Zebulon non-LTR	Tetraodon
			retrotransposon - a consensus	nigroviridis
			sequence.
NeSL	.	LIN10B_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN11_SM	Non-LTR retrotransposon:	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN13_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN14_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN15_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN2_SM	Non-LTR retrotransposon	Schmidtea
			(consensus).	mediterranea
NeSL	.	LIN21_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN23_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN24_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN24B_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN25_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN26_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN3_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN4_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN4b_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN5_SM	Non-LTR retrotransposon from	Schmidtea
			Schmidtea mediterranea:	mediterranea
			consensus.
NeSL	.	LIN6_SM	Non-LTR retrotransposon from	Schmidtea
			Schmidtea mediterranea:	mediterranea
			consensus.
NeSL	.	LIN7_SM	Non-LTR retrotransposon from	Schmidtea
			Schmidtea mediterranea:	mediterranea
			consensus.
NeSL	.	LIN7B_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	LIN9_SM	Non-LTR retrotransposon:	Schmidtea
			consensus.	mediterranea
CRE	JQ747487	MoTeR1	Telomere-specific non-LTR	Magnaporthe oryzae
			retrotransposon MoTeR1 from
			Magnaporthe oryzae.
CRE	JQ747488	MoTeR2	Telomere-specific non-LTR	Magnaporthe oryzae
			retrotransposon MoTeR2 from
			Magnaporthe oryzae.
NeSL	Z82058	NeSL-1	NeSL-1 is a non-LTR	Caenorhabditis
			retrotransposon, complete	elegans
			sequence.
NeSL	.	NeSL-1_C11	A family of NeSL non-LTR	Caenorhabditis
			retrotransposons.	tropicalis
NeSL	.	NeSL-1_CA	A family of NeSL non-LTR	Caenorhabditis
			retrotransposons.	angaria
NeSL	.	NeSL-1_CBre	A family of NeSL non-LTR	Caenorhabditis
			retrotransposons - consensus.	brenneri
NeSL	.	NeSL-1_CBri	A family of NeSL non-LTR	Caenorhabditis
			retrotransposons.	briggsae
NeSL	.	NeSL-1_CJap	A family of NeSL non-LTR	Caenorhabditis
			retrotransposons - consensus.	japonica
NeSL	.	NeSL-1_CRem	A family of NeSL non-LTR	Caenorhabditis
			retrotransposons - consensus.	remanei
NeSL	.	NeSL-1_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	NeSL-1_TV	A family of NeSL non-LTR	Trichomonas
			retrotransposons - consensus.	vaginalis
NeSL	.	NeSL-2_CBre	A family of NeSL non-LTR	Caenorhabditis
			retrotransposons - consensus.	brenneri
NeSL	.	NeSL-2_CRem	A family of NeSL non-LTR	Caenorhabditis
			retrotransposons - consensus.	remanei
NeSL	.	NeSL-2_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
NeSL	.	NeSL-3_CBre	A family of NeSL non-LTR	Caenorhabditis
			retrotransposons - consensus.	brenneri
NeSL	.	NeSL-3_CRem	A family of NeSL non-LTR	Caenorhabditis
			retrotransposons - consensus.	remanei
NeSL	chrUn	NeSL-4_CRem	A family of NeSL non-LTR	Caenorhabditis
			retrotransposons.	remanei
NeSL	.	NeSL-4_SM	Non-LTR retrotransposon;	Schmidtea
			consensus.	mediterranea
R2	BN000800	PERERE-9	Schistosoma mansoni Perere-9	Schistosoma mansoni
			non-LTR retrotransposon (EST).
R4	.	Plat_R4	R4 Non-LTR Retrotransposon	Ornithorhynchus
			from Ornithorhynchus.
R2	AF015815	R2_AM	Anurida maritima	Anurida maritima
			retrotransposon R2, complete
			sequence.
R2	M16558	R2_BM	Bombyx mori rDNA insertion	Bombyx mori
			element R2 (type II),
			complete cds.
R2	AB097121	R2_CI	R2-type LINE.	Ciona intestinalis
R2	.	R2_CPB	Non-LTR retrotransposon:	Chrysemyspicta
			consensus.	bellii
R2	.	R2_DAn	28S rDNA-specific non-LTR	Drosophila
			retrotransposon R2 in	ananassae
			Drosophila ananassae.
R2	X51967	R2_DM	LINE-like retrotransposable	Drosophila
			element R2DM.	melanogaster
R2	.	R2_DPe	28S rDNA-specific non-LTR	Drosophila
			retrotransposon R2 in	persimilis
			Drosophila persimilis.
R2	.	R2_DPs	28S rDNA-specific non-LTR	Drosophila
			retrotransposon R2 in	pseudoobscura
			Drosophila pseudoobscura.
R2	.	R2_DSe	28S rDNA-specific non-LTR	Drosophila
			retrotransposon R2 in	sechellia
			Drosophila sechellia.
R2	.	R2_DSi	28S rDNA-specific non-LTR	Drosophila
			retrotransposon R2 in	simulans
			Drosophila simulans.
R2	.	R2_DYa	28S rDNA-specific non-LTR	Drosophila yakuba
			retrotransposon R2 in
			Drosophila yakuba.
R2	AF015819	R2_FA	Forficula auricularia	Forficula
			retrotransposon R2, complete	auricularia
			sequence.
R2	AF015816	R2_HC	Hippodamia convergens	Hippodamia
			retrotransposon R2 reverse	convergens
			transcriptase gene, partial cds.
R2	GU949558	R2_KF	28S rDNA-specific non-LTR	Kalotermes
			retrotransposon R2 from	flavicollis
			Kalotermes flavicollis.
R2	AF015814	R2_LP	Limulus polyphemus	Limulus polyphemus
			retrotransposon R2, complete
			sequence.
R2	AF015818	R2_PS	Porcellio scaber	Porcellio scaber
			retrotransposon R2, complete
			sequence.
R2	GU949555	R2_RL	28S rDNA-specific non-LTR	Reticulitermes
			retrotransposon R2 from	lucifugus
			Reticulitermes lucifugus.
R2	GU949554	R2_RU	28S rDNA-specific non-LTR	Reticulitermes
			retrotransposon R2 from	urbis
			Reticulitermes urbis.
R2	.	R2-1_AAm	R2 non-LTR retrotransposon	Amblyomma
			from lone star tick.	americanum
R2	.	R2-1_ACC	R2 non-LTR retrotransposon	Aquila chrysaetos
			from golden eagle.	canadensis
R2	.	R2-1_ACh	R2 non-LTR retrotransposon	Acanthisitta
			from rifleman.	chloris
R2	.	R2-1_AFo	R2 non-LTR retrotransposon	Aptenodytes
			from emperor penguin.	forsteri
R2	.	R2-1_AMi	R2-type non-LTR retrotransposon.	Alligator
				mississippiensis
R2	.	R2-1_AOM	R2 non-LTR retrotransposon	Apteryx spp.
			from kiwi.
R2	.	R2-1_ApA	R2 non-LTR retrotransposon	Apteryx australis
			from north island brown kiwi.	mantelli
R2	.	R2-1_APi	R2 non-LTR retrotransposon	Acyrthosiphon
			from pea aphid.	pisum
R2	.	R2-1_BRG	R2 non-LTR retrotransposon	Balearica
			from East African grey	regulorum
			crowned crane.	gibbericeps
R2	.	R2-1_BTe	R2 non-LTR retrotransposon	Bombus terrestris
			from buff-tailed bumblebee.
R2	.	R2-1_CAnn	R2 non-LTR retrotransposon	Calypte anna
			from Anna's hummingbird.
R2	.	R2-1_CAu	R2 non-LTR retrotransposon	Cathartes aura
			from turkey vulture.
R2	.	R2-1_CBr	R2 non-LTR retrotransposon	Corvus
			from American crow.	brachyrhynchos
R2	.	R2-1_CCa	R2 non-LTR retrotransposon	Antrostomus
			from chuck-will's-widow.	carolinensis
R2	.	R2-1_CCan	R2 non-LTR retrotransposon	Cuculus canorus
			from common cuckoo.
R2	.	R2-1_CPu	R2 non-LTR retrotransposon	Calidris pugnax
			from ruff.
R2	.	R2-1_Crp	Non-LTR retrotransposon.	Crocodylus porosus
R2	.	R2-1_CSt	R2 non-LTR retrotransposon	Colius striatus
			from speckled mousebird.
R2	.	R2-1_CU	R2 non-LTR retrotransposon	Chlamydotis
			from MacQueen's bustard.	macqueenii
R2	.	R2-1_CVo	R2 non-LTR retrotransposon	Charadrius
			from killdeer.	vociferus
R2	.	R2-1_DWi	28S rDNA-specific non-LTR	Drosophila
			retrotransposon R2 in	willistoni
			Drosophila willistoni.
R2	.	R2-1_EGa	R2 non-LTR retrotransposon	Egretta garzetta
			from little egret.
R2	.	R2-1_FAl	R2 non-LTR retrotransposon	Ficedula
			from collared flycatcher.	albicollis
R2	.	R2-1_FCh	R2 non-LTR retrotransposon	Falco cherrug
			from Saker falcon.
R2	.	R2-1_FPe	R2 non-LTR retrotransposon	Falco peregrinus
			from peregrine falcon.
R2	.	R2-1_GA	R2 non-LTR retrotransposon	Gasterosteus
			from three-spined stickleback.	aculeatus
R2	.	R2-1_Gav	Non-LTR retrotransposon.	Gavialis
				gangeticus
R2	.	R2-1_GFo	R2 non-LTR retrotransposon	Geospiza fortis
			from medium ground finch.
R2	.	R2-1_GSt	R2 non-LTR retrotransposon	Gavia stellata
			from red-throated loon.
R2	.	R2-1_HAl	R2 non-LTR retrotransposon	Haliaeetus
			from white-tailed eagle.	albicilla
R2	.	R2-1_IS	R2 non-LTR retrotransposon	Ixodes scapularis
			from deer tick.
R2	.	R2-1_LCh	R2-type non-LTR	Latimeria
			retrotransposon - consensus.	chalumnae
R2	.	R2-1_LDi	R2 non-LTR retrotransposon	Leptosomus
			from cuckoo roller.	discolor
R2	.	R2-1_LSal	non-LTR retrotransposon,	Lepeophtheirus
			consensus.	salmonis
R2	.	R2-1_LV	R2 non-LTR retrotransposon	Lytechinus
			from green sea urchin.	variegatus
R2	.	R2-1_MDe	R2 non-LTR retrotransposon	Mayetiola
			from Hessian fly.	destructor
R2	.	R2-1_MLe	R2 non-LTR retrotransposon -	Mnemiopsis leidyi
			consensus.
R2	.	R2-1_MR	R2 non-LTR retrotransposon	Megachile
			from alfalfa leafcutter bee.	rotundata
R2	.	R2-1_MUn	R2 non-LTR retrotransposon	Melopsittacus
			fragment from budgerigar.	undulatus
R2	.	R2-1_MUni	R2 non-LTR retrotransposon	Mesitornis
			from brown mesite.	unicolor
R2	.	R2-1_MVi	R2 non-LTR retrotransposon	Manacus vitellinus
			from golden-collared manakin.
R2	.	R2-1_NNi	R2 non-LTR retrotransposon	Nipponia nippon
			from created ibis.
R2	.	R2-1_NV	Starlet sea anemone R2-1_NV	Nematostella
			autonomous Non-LTR	vectensis
			Retrotransposon - consensus.
R2	.	R2-1_OHo	R2 non-LTR retrotransposon	Opisthocomus
			from hoatzin.	hoazin
R2	.	R2-1_PAd	R2 non-LTR retrotransposon	Pygoscelis adeliae
			from Adelie penguin.
R2	.	R2-1_PBa	R2 non-LTR retrotransposon	Pogonomyrmex
			from red harvester ant.	barbatus
R2	.	R2-1_PCar	R2 non-LTR retrotransposon	Phalacrocorax
			from great cormorant.	carbo
R2	.	R2-1_PCau	R2 non-LTR retrotransposon	Priapulus caudatus
			sequence.
R2	.	R2-1_PCr	R2 non-LTR retrotransposon	Podiceps cristatus
			from great crested grebe.
R2	.	R2-1_PCri	R2 non-LTR retrotransposon	Pelecanus crispus
			from Dalmatian pelican.
R2	.	R2-1_PGu	R2 non-LTR retrotransposon	Pterocles
			from sandgrouse.	gutturalis
R2	.	R2-1_PLe	R2 non-LTR retrotransposon	Phaethon lepturus
			from tropicbird.
R2	.	R2-1_PM	R2-1_PM is a family of R2	Petromyzon marinus
			non-LTR retrotransposons -
			consensus.
R2	.	R2-1_PPap	R2 non-LTR retrotransposon	Phlebotomus
			from sand fly.	papatasi
R2	.	R2-1_PPu	R2 non-LTR retrotransposon	Picoides pubescens
			from downy woodpecker.
R2	.	R2-1_PRR	R2 non-LTR retrotransposon	Phoenicopterus
			from American flamingo.	ruber ruber
R2	.	R2-1_PSi	R2 non-LTR retrotransposon	Pelodiscus
			from Chinese soft-shelled	sinensis
			turtle.
R2	.	R2-1_RMi	R2 non-LTR retrotransposon	Rhipicephaus
			from brown tick.	microplus
R2	.	R2-1_RPr	R2 non-LTR retrotransposon	Rhodnius prolixus
			sequence.
R2	.	R2-1_RPu	R2 non-LTR retrotransposon	Rhipicephalus
			cDNA sequence from brown tick.	pulchellus
R2	.	R2-1_SCa	R2 non-LTR retrotransposon	Serinus canaria
			from Atlantic canary.
R2	.	R2-1_SK	R2 non-LTR retrotransposon	Saccoglossus
			from acorn worm.	kowalevskii
R2	.	R2-1_SM	R2-type retrotransposon from	Schmidtea
			Schmidtea mediterranea:	mediterranea
			consensus.
R2	.	R2-1_SP	R2 non-LTR retrotransposon	Strongylocentrotus
			from purple sea urchin.	purpuratus
R2	AGKD01072455	R2-1_SSa	R2-type non-LTR retrotransposon.	Salmo salar
R2	.	R2-1_StC	R2 non-LTR retrotransposon	Struthiocamelus
			from ostrich.	australis
R2	.	R2-1_TAl	R2 non-LTR retrotransposon	Tyto alba
			from barn owl.
R2	.	R2-1_TCas	R2 non-LTR retrotransposon	Tribolium
			from red flour beetle - consensus	castaneum
R2	.	R2-1_TG	A family of R2 non-LTR	Taeniopygia
			retrotransposons - consensus	guttata
			sequence.
R2	.	R2-1_TGut	R2 non-LTR retrotransposon	Tinamus guttatus
			from white-throated tinamou.
R2	.	R2-1_TSP	A family of R2 non-LTR	Trichinella
			retrotransposons in the	spiralis
			Trichinella spiralis genome -
			a consensus.
R2	scaffold_6	R2-1_TUr	R2 non-LTR retrotransposon	Tetranychus
			from twospotted spider mite.	urticae
R2	.	R2-1_XM	R2 non-LTR retrotransposon	Xiphophorus
			fragment from Southern	maculatus
			platyfish.
R2	.	R2-1_ZA	R2 non-LTR retrotransposon	Zonotrichia
			from white-throated sparrow.	albicollis
R2	.	R2-1_ZLM	R2 non-LTR retrotransposon	Zosterops
			from silvereye.	lateralis
				melanops
R2	.	R2-2_APi	R2 non-LTR retrotransposon	Acyrthosiphon
			from pea aphid.	pisum
R2	.	R2-2_CCan	R2 non-LTR retrotransposon	Cuculus canorus
			from common cuckoo.
R2	.	R2-2_CMa	R2 non-LTR retrotransposon	Chlamydotis
			from Macqueen's bustard.	macqueenii
R2	.	R2-2_DWi	28S rDNA-specific non-LTR	Drosophila
			retrotransposon R2 in	willistoni
			Drosophila willistoni.
R2	.	R2-2_HAl	R2 non-LTR retrotransposon	Haliaeetus
			from white-tailed eagle.	albicilla
R2	.	R2-2_IS	R2 non-LTR retrotransposon	Ixodes scapularis
			from deer tick.
R2	.	R2-2_MR	R2 non-LTR retrotransposon	Megachile
			from alfalfa leafcutter bee.	rotundata
R2	.	R2-2_MUn	R2 non-LTR retrotransposon	Melopsittacus
			fragment from budgerigar.	undulatus
R2	.	R2-2_MUni	R2 non-LTR retrotransposon	Mesitornis
			from brown mesite.	unicolor
R2	.	R2-2_NNi	R2 non-LTR retrotransposon	Nipponia nippon
			from created ibis.
R2	.	R2-2_NV	Starlet sea anemone R2-2_NV	Nematostella
			autonomous Non-LTR	vectensis
			Retrotransposon - consensus.
R2	.	R2-2_PBa	R2 non-LTR retrotransposon	Pogonomyrmex
			from red harvester ant.	barbatus
R2	.	R2-2_PM	R2-2_PM is a family of R2	Petromyzon marinus
			non-LTR retrotransposons - a
			consensus.
R2	.	R2-2_RPr	R2 non-LTR retrotransposon	Rhodnius prolixus
			sequence.
R2	.	R2-2_SMed	R2 non-LTR retrotransposon	Schmidtea
			from Schmidtea mediterranea:	mediterranea
			consensus.
R2	.	R2-2_TCas	R2 non-LTR retrotransposon	Tribolium
			from red flour beetle.	castaneum
R2	scaffold_37	R2-2_TUr	R2 non-LTR retrotransposon	Tetranychus
			from twospotted spider mite.	urticae
R2	ABJB010555169	R2-3_IS	R2 non-LTR retrotransposon	Ixodes scapularis
			from deer tick.
R2	.	R2-3_MR	R2 non-LTR retrotransposon	Megachile
			from alfalfa leafcutter bee.	rotundata
R2	.	R2-4_MR	R2 non-LTR retrotransposon	Megachile
			from alfalfa leafcutter bee.	rotundata
R2	.	R2-5_MR	R2 non-LTR retrotransposon	Megachile
			from alfalfa leafcutter bee.	rotundata
R2	.	R2-6_MR	R2 non-LTR retrotransposon	Megachile
			from alfalfa leafcutter bee.	rotundata
R2	.	R2-7_MR	R2 non-LTR retrotransposon	Megachile
			from alfalfa leafcutter bee.	rotundata
R2	.	R2-8_MR	R2 non-LTR retrotransposon	Megachile
			from alfalfa leafcutter bee.	rotundata
R2	.	R2-N1_Gav	Non-LTR retrotransposon.	Gavialis
				gangeticus
R2	.	R2-N2_Gav	Non-LTR retrotransposon.	Gavialis
				gangeticus
R2	.	R2-N2B_Gav	Non-LTR retrotransposon.	Gavialis
				gangeticus
R2	.	R2A_NVi	28S rDNA-specific non-LTR	Nasonia
			retrotransposon R2 in	vitripennis
			Nasonia vitripennis.
R2	AF015817	R2A_TM	Tenebrio molitor	Tenebrio molitor
			retrotransposon R2 reverse
			transcriptase gene, partial cds.
R2	.	R2Amel	R2Amel - R2 non-LTR	Apis mellifera
			retrotransposon from the
			honeybee Apis mellifera.
R2	AF015685	R2B_DM	Drosophila mercatorum R2	Drosophila
			retrotransposon reverse	mercatorum
			transcriptase domain protein
			gene, complete cds.
R2	.	R2B_NVi	28S rDNA-specific non-LTR	Nasonia
			retrotransposon R2 in	vitripennis
			Nasonia vitripennis.
R2	AF015822	R2B_TM	Tenebrio molitor	Tenebrio molitor
			retrotransposon R2 reverse
			transcriptase gene, partial cds.
R2	.	R2C_NGi	28S rDNA-specific non-LTR	Nasonia giraulti
			retrotransposon R2 in
			Nasonia giraulti.
R2	AB097122	R2Ci-B	Ciona intestinalis	Ciona intestinalis
			retrotransposon R2Ci-B,
			complete sequence.
R2	.	R2Ci-D	Ciona intestinalis	Ciona intestinalis
			retrotransposon R2CiD,
			complete sequence.
R2	AB097121	R2CIA_CI	Ciona intestinalis	Ciona intestinalis
			retrotransposon R2Ci-A,
			complete sequence.
R2	AB097125	R2Cs-D	Ciona intestinalis	Ciona savignyi
			retrotransposon R2CsD,
			partial sequence.
R2	.	R2D_NGi	28S rDNA-specific non-LTR	Nasonia giraulti
			retrotransposon R2 in
			Nasonia giraulti.
R2	NM_001030097	R2Dr	R2 non-LTR retrotransposon in	Danio rerio
			the Danio rerio
			genome - a single copy.
R2	.	R2E_NLo	28S rDNA-specific non-LTR	Nasonia
			retrotransposon R2 in	longicornis
			Nasonia longicornisi.
R2	AB201408	R2Eb	R2 non-LTR retrotransposon	Eptatretus burgeri
			from Eptatretus burgeri.
R2	AB201415	R2Ha	R2 non-LTR retrotransposon	Hasarius adansoni
			from Hasarius adansoni.
R2	JN937617	R2La	R2-type non-LTR retrotransposon.	Lepidurus arcticus
R2	.	R2LcA	R2-type non-LTR retrotransposon.	Lepidurus couesii
R2	JN937619	R2LcB	R2-type non-LTR retrotransposon.	Lepidurus couesii
R2	.	R2LcC	R2-type non-LTR retrotransposon.	Lepidurus couesii
R2	JN937616	R2Ll	R2-type non-LTR retrotransposon.	Lepidurus apus
				lubbocki
R2	AB201414	R2Mr	R2 non-LTR retrotransposon	Metacrinus
			from Metacrinus rotundus.	rotundus
R2	.	R2NS-1_CGi	R2-type retrotransposon from	Crassostrea gigas
			Crassostrea gigas.
R2	.	R2NS-1_CSi	R2-type retrotransposon from	Clonorchis
			Clonorchis sinensis: consensus.	sinensis
R2	.	R2NS-1_PMi	R2-like non-LTR	Patiria miniata
			retrotransposon from bat star.
R2	.	R2NS-1_SMed	R2-type retrotransposon from	Schmidtea
			Schmidtea mediterranea:	mediterranea
			consensus.
R2	.	R2Nvec-A	R2Nvec-A - R2 non-LTR	Nematostella
			retrotransposon from the	vectensis
			starlet sea anemone
			Nematostella vectensis.
R2	.	R2Ol-A	R2 non-LTR retrotransposon	Oryzias latipes
			from the medaka
			Oryzias latipes - consensus.
R2	AB201416	R2Pc	R2 non-LTR retrotransposon	Procambarus
			from Procambarus clarkii.	clarkii
R2	.	R2Sm-A	R2Sm-A - R2 non-LTR	Schistosoma
			retrotransposon from the	mansoni
			bloodfluke Schistosoma
			mansoni.
R2	AB201409	R2Ta	R2 non-LTR retrotransposon	Tanichthys
			from Tanichthys albonubes.	albonubes
R2	EU854578	R2Tc	R2-type non-LTR retrotransposon.	Triops
				cancriformis
R2	JN937621	R2Tc_it	R2-type non-LTR retrotransposon.	Triops
				cancriformis
R2	AB201417	R2Tl	R2 non-LTR retrotransposon	Triops
			from Triops longicaudatus.	longicaudatus
R4	U29445	R4_AL	Ascaris lumbricoides	Ascaris
			site-specific non-LTR	lumbricoides
			retrotransposable element R4
			in 26S rDNA, complete sequence.
R4	U29590	R4_HC	Haemonchus contortus non-LTR	Haemonchus
			retrotransposon specific to	contortus
			the large subunit rRNA genes
			of nematodes.
R4	.	R4_Hmel	a R4 element from Heliconius	Heliconius
			melpomene.	melpomene
R4	.	R4-1_AC	A family of R4 non-LTR	Anolis
			retrotransposons - consensus	carolinensis
			sequence.
R4	.	R4-1_ADi	R4-type retrotransposon:	Acropora
			consensus.	digitifera
R4	.	R4-1_BM	Non-LTR retrotransposon - a	Bombyx mori
			consensus.
R4	CADV01008175	R4-1_BX	An R4 non-LTR retrotransposon	Bursaphelenchus
			family from Bursaphelenchus	xylophilus
			xylophilus.
R4	ABLE03011482	R4-1_CJap	An R4 non-LTR retrotransposon	Caenorhabditis
			family from Caenorhabditis	japonica
			japonica.
R4	.	R4-1_CM	Non-LTR retrotransposon from	Callorhinchus
			the elephant shark - consensus.	milii
R4	.	R4-1_CPB	Non-LTR retrotransposon:	Chrysemyspicta
			consensus.	bellii
R4	.	R4-1_ED	Autonomous non-LTR	Entamoeba dispar
			retrotransposon from the R4
			clade - a consensus sequence.
R4	.	R4-1_HG	An R4 non-LTR retrotransposon	Heterodera
			family from	glycines
			Heterodera glycines.
R4	.	R4-1_HMe	Non-LTR retrotransposon family from	Heliconius
			Heliconius melpomene melpomene.	melpomene
				melpomene
R4	CABB01003843	R4-1_MI	An R4 non-LTR retrotransposon	Meloidogyne
			family from Meloidogyne	incognita
			incognita.
R4	.	R4-1_PH	Non-LTR Retrotransposon,	Parhyale
			consensus.	hawaiensis
R4	CACX01002001	R4-1_SRa	An R4 non-LTR retrotransposon	Strongyloides
			family from Strongyloides ratti.	ratti
R4	.	R4-1_TCa	R4-type retrotransposon:	Tribolium
			consensus.	castaneum
R4	.	R4-1B_AC	Dong-type non-LTR	Anolis
			retrotransposons - a consensus	carolinensis
			sequence.
R4	.	R4-2_AS	An R4 non-LTR retrotransposon	Ascaris suum
			family from Ascaris suum.
R4	CADV01009048	R4-2_BX	An R4 non-LTR retrotransposon	Bursaphelenchus
			family from Bursaphelenchus	xylophilus
			xylophilus.
R4	ABLA01000389	R4-2_HG	An R4 non-LTR retrotransposon	Heterodera
			family from Heterodera	glycines
			glycines.
R4	CACX01002006	R4-2_SRa	An R4 non-LTR retrotransposon	Strongyloides
			family from Strongyloides ratti.	ratti
R4	CADV01008832	R4-3_BX	An R4 non-LTR retrotransposon	Bursaphelenchus
			family from Bursaphelenchus	xylophilus
			xylophilus.
R4	.	R4-3_SRa	An R4 non-LTR retrotransposon	Strongyloides
			family from Strongyloides ratti.	ratti
R4	.	R4-4_BX	An R4 non-LTR retrotransposon	Bursaphelenchus
			family from Bursaphelenchus	xylophilus
			xylophilus.
R4	.	R4-4_SRa	An R4 non-LTR retrotransposon	Strongyloides
			family from Strongyloides	ratti
			ratti.
R4	.	R4-5_BX	An R4 non-LTR retrotransposon	Bursaphelenchus
			family from Bursaphelenchus	xylophilus
			xylophilus.
NeSL	AY216701	R5	Girardia tigrina R5	Girardia tigrina
			retrotransposon, complete
			sequence.
NeSL	.	R5-1_SM	A family of planarian NeSL	Schmidtea
			non-LTR retrotransposons -	mediterranea
			consensus.
NeSL	.	R5-2_SM	A family of planarian NeSL	Schmidtea
			non-LTR retrotransposons -	mediterranea
			consensus.
R2	.	R8Hm-A	R8Hm-A - 18S rDNA-specific	Hydra vulgaris
			non-LTR retrotransposon from
			Hydra magnipapillata.
R2	.	R8Hm-B	R8Hm-B - 18S rDNA-specific	Hydra vulgaris
			non-LTR retrotransposon from
			Hydra magnipapillata.
R2	.	R9Av	R9Av, an rDNA-specific non-LTR	Adineta vaga
			retrotransposon family from
			rotifer.
R2	FJ461304	RaR2	28S rDNA-specific non-LTR	Rhynchosciara
			retrotransposon R2 from	americana
			Rhynchosciara americana.
R4	.	Rex6	Non-LTR retrotransposon;	Takifugu rubripes
			site-specific LINE; R4/Dong
			superfamily; REX6; DONG_FR.
R4	.	Rex6-1_OL	A Rex6 non-LTR retrotransposon	Oryzias latipes
			family from Olyzias latipes.
CRE	X17078	SLACS	Trypanosoma brucei DNA for	Trypanosoma brucei
			retrotransposable element SLACS.
NeSL	.	Utopia-1_ACa	Utopia-1_ACa is a protozoan	Acanthamoeba
			Utopia non-LTR retrotransposon -	castellanii
			a complete sequence.
NeSL	scaffold_474	Utopia-1_ACar	A family of NeSL non-LTR	Anolis
			retrotransposons.	carolinensis
NeSL	.	Utopia-1_AEc	A family of Utopia non-LTR	Acromyrmex
			retrotransposons - consensus.	echinatior
NeSL	.	Utopia-1_AMi	A family of NeSL non-LTR	Alligator
			retrotransposons - consensus.	mississippiensis
NeSL	.	Utopia-1_APi	A family of Utopia non-LTR	Acyrthosiphon
			retrotransposons - consensus.	pisum
NeSL	.	Utopia-1_APl	A family of Utopia non-LTR	Agrilus
			retrotransposons.	planipennis
NeSL	.	Utopia-1_CFl	A family of Utopia non-LTR	Camponotus
			retrotransposons - consensus.	floridanus
NeSL	.	Utopia-1_CMy	A family of Utopia non-LTR	Chelonia mydas
			retrotransposons - consensus.
NeSL	.	Utopia-1_CPB	A family of Utopia non-LTR	Chrysemyspicta
			retrotransposons - consensus.	bellii
NeSL	.	Utopia-1_Crp	Non-LTR retrotransposon.	Crocodylus porosus
NeSL	.	Utopia-1_DPo	A family of Utopia non-LTR	Dendroctonus ponderosae
			retrotransposons.
NeSL	.	Utopia-1_DPu	A family of Utopia non-LTR	Daphnia pulex
			retrotransposons - consensus.
NeSL	.	Utopia-1_DYak	A family of Utopia non-LTR	Drosophila yakuba
			retrotransposons - consensus.
NeSL	.	Utopia-1_EBr	A family of Utopia non-LTR	Eimeria brunetti
			retrotransposons - consensus.
NeSL	.	Utopia-1_EMi	A family of Utopia non-LTR	Eimeria mitis
			retrotransposons - consensus.
NeSL	.	Utopia-1_ENe	A family of Utopia non-LTR	Eimeria necatrix
			retrotransposons - consensus.
NeSL	.	Utopia-1_Gav	Non-LTR retrotransposon.	Gavialis
				gangeticus
NeSL	.	Utopia-1_GG1	A family of Utopia non-LTR	Ganaspis
			retrotransposons.
NeSL	.	Utopia-1_HAra	A family of Utopia non-LTR	Hyaloperonospora
			retrotransposons.	arabidopsidis
NeSL	.	Utopia-1_HG	A family of Utopia non-LTR	Heterodera
			retrotransposons.	glycines
NeSL	.	Utopia-1_HMM	A family of Utopia non-LTR	Heliconius
			retrotransposons.	melpomene
				melpomene
NeSL	.	Utopia-1_HSal	A family of Utopia non-LTR	Harpegnathos
			retrotransposons - consensus.	saltator
NeSL	.	Utopia-1_IS	A family of Utopia non-LTR	Ixodes scapularis
			retrotransposons - consensus.
NeSL	.	Utopia-1_LAl	A family of Utopia non-LTR	Lasioglossum
			retrotransposons.	albipes
NeSL	.	Utopia-1_LFu	A family of Utopia non-LTR	Ladona fulva
			retrotransposons.
NeSL	AGCV01358106	Utopia-1_LV	A family of Utopia non-LTR	Lytechinus
			retrotransposons.	variegatus
NeSL	.	Utopia-1_MRo	A family of Utopia non-LTR	Megachile
			retrotransposons - consensus.	rotundata
NeSL	.	Utopia-1_NVit	A family of Utopia non-LTR	Nasonia
			retrotransposons - consensus.	vitripennis
NeSL	.	Utopia-1_PAlni	NeSL non-LTR retrotransposon	Phytophthora alni
			from Phytophthora alni.
NeSL	.	Utopia-1_PArrh	NeSL non-LTR retrotransposon	Pythium
			from Pythium arrhenomanes.	arrhenomanes
NeSL	.	Utopia-1_PBa	A family of Utopia non-LTR	Pogonomyrmex
			retrotransposons - consensus.	barbatus
NeSL	.	Utopia-1_PCa	A family of Utopia non-LTR	Phytophthora
			retrotransposons - consensus.	capsici
NeSL	.	Utopia-1_PCinn	NeSL non-LTR retrotransposon	Phytophthora
			from Phytophthora cinnamomi.	cinnamomi
NeSL	AHJF01004292	Utopia-1_PCu	A family of Utopia non-LTR	Pseudoperonospora
			retrotransposons - consensus.	cubensis
NeSL	.	Utopia-1_PI	A family of NeSL non-LTR	Phytophthora
			retrotransposons - consensus.	infestans
NeSL	.	Utopia-1_PInsi	NeSL non-LTR retrotransposon	Pythium insidiosum
			from Pythium insidiosum.
NeSL	.	Utopia-1_PKern	NeSL non-LTR retrotransposon	Phytophthora
			from Phytophthora kernoviae.	kernoviae
NeSL	.	Utopia-1_PLate	NeSL non-LTR retrotransposon	Phytophthora
			from Phytophthora lateralis.	lateralis
NeSL	.	Utopia-1_PMi	A family of Utopia non-LTR	Patiria miniata
			retrotransposons.
NeSL	.	Utopia-1_PPac	A family of Utopia non-LTR	Pristionchus
			retrotransposons.	pacificus
NeSL	.	Utopia-1_PPini	NeSL non-LTR retrotransposon	Phytophthora
			from	pinifolia
			Phytophthora pinifolia.
NeSL	.	Utopia-1_PR	A family of Utopia non-LTR	Phytophthora
			retrotransposons - consensus.	ramorum
NeSL	.	Utopia-1_PRe	A family of Utopia non-LTR	Panagrellus
			retrotransposons - consensus.	redivivus
NeSL	.	Utopia-1_PS	A family of Utopia non-LTR	Phytophthora sojae
			retrotransposons - consensus.
NeSL	.	Utopia-1_PSi	A family of Utopia non-LTR	Pelodiscus
			retrotransposons - consensus.	sinensis
NeSL	.	Utopia-1_PT	A family of Utopia non-LTR	Parasteatoda
			retrotransposons.	tepidariorum
NeSL	ADOS01001321	Utopia-1_PU	A family of Utopia non-LTR	Pythium ultimum
			retrotransposons.
NeSL	.	Utopia-1_PVexa	NeSL non-LTR retrotransposon	Phytopythium
			from Phytopythium vexans.	aff. vexans
NeSL	.	Utopia-1_SaPa	A family of Utopia non-LTR	Saprolegnia
			retrotransposons.	parasitica
NeSL	.	Utopia-1_SDicl	NeSL non-LTR retrotransposon	Saprolegnia
			from Saprolegnia diclina.	diclina
NeSL	.	Utopia-1_SM	A family of Utopia non-LTR	Strigamia maritima
			retrotransposons.
NeSL	AAGJ02140537	Utopia-1_SP	A family of Utopia non-LTR	Strongylocentrotus
			retrotransposons.	purpuratus
NeSL	.	Utopia-1_TSP	A family of Utopia non-LTR	Trichinella
			retrotransposons.	spiralis
NeSL	.	Utopia-1B_CPB	A family of Utopia non-LTR	Chrysemys picta
			retrotransposons - consensus.	bellii
NeSL	.	Utopia-2_APi	A family of Utopia non-LTR	Acyrthosiphon
			retrotransposons.	pisum
NeSL	.	Utopia-2_CMy	A family of Utopia non-LTR	Chelonia mydas
			retrotransposons - consensus.
NeSL	.	Utopia-2_CPB	A family of Utopia non-LTR	Chrysemys picta
			retrotransposons - consensus.	bellii
NeSL	.	Utopia-2_DPu	A family of Utopia non-LTR	Daphnia pulex
			retrotransposons.
NeSL	.	Utopia-2_LFu	A family of Utopia non-LTR	Ladona fulva
			retrotransposons.
NeSL	.	Utopia-2_PCa	A family of Utopia non-LTR	Phytophthora
			retrotransposons - consensus.	capsici
NeSL	.	Utopia-2_PI	A family of NeSL non-LTR	Phytophthora
			retrotransposons - consensus.	infestans
NeSL	.	Utopia-2_PR	A family of Utopia non-LTR	Phytophthora
			retrotransposons - consensus.	ramorum
NeSL	.	Utopia-2_PS	A family of Utopia non-LTR	Phytophthora sojae
			retrotransposons - consensus.
NeSL	.	Utopia-2_PU	A family of Utopia non-LTR	Pythium ultimum
			retrotransposons.
NeSL	.	Utopia-3_CPB	A family of Utopia non-LTR	Chrysemys picta
			retrotransposons - consensus.	bellii
NeSL	.	Utopia-3_DPu	A family of Utopia non-LTR	Daphnia pulex
			retrotransposons.
NeSL	.	Utopia-3_LFu	A family of Utopia non-LTR	Ladona fulva
			retrotransposons.
NeSL	.	Utopia-3_PCa	A family of Utopia non-LTR	Phytophthora
			retrotransposons - consensus.	capsici
NeSL	.	Utopia-3_PI	A family of NeSL non-LTR	Phytophthora
			retrotransposons - consensus.	infestans
NeSL	.	Utopia-3_PR	A family of Utopia non-LTR	Phytophthora
			retrotransposons - consensus.	ramorum
NeSL	.	Utopia-4_LFu	A family of Utopia non-LTR	Ladona fulva
			retrotransposons.
NeSL	AATU01001281.1	Utopia-4_PI	A family of NeSL non-LTR	Phytophthora
			retrotransposons - a copy.	infestans
NeSL	.	Utopia-4_PR	A family of Utopia non-LTR	Phytophthora
			retrotransposons - consensus.	ramorum
NeSL	.	Utopia-5_LFu	A family of Utopia non-LTR	Ladona fulva
			retrotransposons.
NeSL	.	Utopia-5_PI	A family of Utopia non-LTR	Phytophthora
			retrotransposons - consensus.	infestans
NeSL	.	Utopia-5_PR	A family of Utopia non-LTR	Phytophthora
			retrotransposons - consensus.	ramorum
NeSL	.	Utopia-6_LFu	A family of Utopia non-LTR	Ladona fulva
			retrotransposons.
R4	.	X4_LINE	Conserved LINE element	Vertebrata
			reconstructed from the human
			genome - consensus.
NeSL	.	YURE_CSa	A NeSL non-LTR retrotransposon	Ciona savignyi
			from Ciona savignyi.
R2	.	YURE-2_Cis	YURE non-LTR retrotransposon	Ciona savignyi
			from Ciona savignyi.
NeSL	.	YURECi	Ciona intestinalis	Ciona intestinalis
			retrotransposon YURECi.

A skilled artisan can, based on the Accession numbers provided in Tables 1-3 determine the nucleic acid and corresponding polypeptide sequences of each retrotransposon and domains thereof, e.g., by using routine sequence analysis tools as Basic Local Alignment Search Tool (BLAST) or CD-Search for conserved domain analysis. Other sequence analysis tools are known and can be found, e.g., at molbiol-tools.ca, for example, at molbiol-tools.ca/Motifs.htm. SEQ ID NOs 1-112 align with each row in Table 1, and SEQ ID NOs 113-1015 align with the first 903 rows of Table 2.

Tables 1-3 herein provide the sequences of exemplary transposons, including the amino acid sequence of the retrotransposase, and sequences of 5′ and 3′ untranslated regions to allow the retrotransposase to bind the template RNA, and the full transposon nucleic acid sequence. In some embodiments, a 5′ UTR of any of Tables 1-3 allows the retrotransposase to bind the template RNA. In some embodiments, a 3′ UTR of any of Tables 1-3 allows the retrotransposase to bind the template RNA. Thus, in some embodiments, a polypeptide for use in any of the systems described herein can be a polypeptide of any of Tables 1-3 herein, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, the system further comprises one or both of a 5′ or 3′ untranslated region of any of Tables 1-3 herein (or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto), e.g., from the same transposon as the polypeptide referred to in the preceding sentence, as indicated in the same row of the same table. In some embodiments, the system comprises one or both of a 5′ or 3′ untranslated region of any of Tables 1-3 herein, e.g., a segment of the full transposon sequence that encodes an RNA that is capable of binding a retrotransposase, and/or the sub-sequence provided in the column entitled Predicted 5′ UTR or Predicted 3′ UTR.

In some embodiments, a polypeptide for use in any of the systems described herein can be a molecular reconstruction or ancestral reconstruction based upon the aligned polypeptide sequence of multiple retrotransposons. In some embodiments, a 5′ or 3′ untranslated region for use in any of the systems described herein can be a molecular reconstruction based upon the aligned 5′ or 3′ untranslated region of multiple retrotransposons. A skilled artisan can, based on the Accession numbers provided herein, align polypeptides or nucleic acid sequences, e.g., by using routine sequence analysis tools as Basic Local Alignment Search Tool (BLAST) or CD-Search for conserved domain analysis. Molecular reconstructions can be created based upon sequence consensus, e.g. using approaches described in Ivics et al., Cell 1997, 501 510; Wagstaff et al., Molecular Biology and Evolution 2013, 88-99. In some embodiments, the retrotransposon from which the 5′ or 3′ untranslated region or polypeptide is derived is a young or a recently active mobile element, as assessed via phylogenetic methods such as those described in Boissinot et al., Molecular Biology and Evolution 2000, 915-928.

Table 3 (below) shows exemplary GENE WRITER™ proteins and associated sequences from a variety of retrotransposases, identified using data mining. Column 1 indicates the family to which the retrotransposon belongs. Column 2 lists the element name. Column 3 indicates an accession number, if any. Column 4 lists an organism in which the retrotransposase is found. Column 5 lists the DNA sequence of the retrotransposon. Column 6 lists the predicted 5′ untranslated region, and column 7 lists the predicted 3′ untranslated region; both are segments of the sequence of column 5 that are predicted to allow the template RNA to bind the retrotransposase of column 8. (It is understood that columns 5-7 show the DNA sequence, and that an RNA sequence according to any of columns 5-7 would typically include uracil rather than thymidine.) Column 8 lists the predicted retrotransposase sequence encoded in the retrotransposon of column 5.

Lengthy table referenced here
US20240318170A1-20240926-T00001
Please refer to the end of the specification for access instructions.

Gene Writers, e.g. Thermostable GENE WRITER™ Genome Editor Polypeptides

While not wishing to be bound by theory, in some embodments, retrotransposases that evolved in cold environments may not function as well at human body temperature. This application provides a number of thermostable GENE WRITER™ genome editor polypeptides, including proteins derived from avian retrotransposases. Exemplary avian transposase sequences in Table 3 include those of Taeniopygia guttata (zebra finch; transposon name R2-1_TG), Geospiza fortis (medium ground finch; transposon name R2-1_Gfo), Zonotrichia albicollis (white-throated sparrow; transposon name R2-1_ZA), and Tinamus guttatus (white-throated tinamou; transposon name R2-1_TGut).

Thermostability may be measured, e.g., by testing the ability of a GENE WRITER™ to polymerize DNA in vitro at a high temperature (e.g., 37° C.) and a low temberature (e.g., 25° C.). Suitable conditions for assaying in vitro DNA polymerization activity (e.g., processivity) are described, e.g., in Bibillo and Eickbush, “High Processivity of the Reverse Transcriptase from a Non-long Terminal Repeat Retrotransposon” (2002) JBC 277, 34836-34845. In some embodiments, the thermostable GENE WRITER™ polypeptide has an activity, e.g., a DNA polymerization activity, at 37° C. that is no less than 70%, 75%, 80%, 85%, 90%, or 95% of its activity at 25° C. under otherwise similar conditions.

In some embodiments, a GENE WRITER™ polypeptide (e.g., a sequence of Table 1, 2, or 3 or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto) is stable in a subject chosen from a mammal (e.g., human) or a bird. In some embodiments, a GENE WRITER™ polypeptide described herein is functional at 37° C. In some embodiments, a GENE WRITER™ polypeptide described herein has greater activity at 37° C. than it does at a lower temperature, e.g., at 30° C., 25° C., or 20° C. In some embodiments, a GENE WRITER™ polypeptide described herein has greater activity in a human cell than in a zebrafish cell.

In some embodiments, a GENE WRITER™ polypeptide is active in a human cell cultured at 37° C., e.g., using an assay of Example 6 or Example 7 herein.

In some embodiments, the assay comprises steps of: (1) introducing HEK293T cells into one or more wells of 6.4 mm diameter, at 10,000 cells/well, (2) incubating the cells at 37° C. for 24 hr, (3) providing a transfection mixture comprising 0.5 μl if FuGENE® HD transfection reagent and 80 ng DNA (wherein the DNA is a plasmid comprising, in order, (a) CMV promoter, (b) 100 bp of sequence homologous to the 100 bp upstream of the target site, (c) sequence encoding a 5′ untranslated region that binds the GENE WRITER™ protein, (d) sequence encoding the GENE WRITER™ protein, (e) sequence encoding a 3′ untranslated region that binds the GENE WRITER™ protein (f) 100 bp of sequence homologous to the 100 bp downstream of the target site, and (g) BGH polyadenylation sequence) and 10 μl Opti-MEM and incubating for 15 min at room temperature, (4) adding the transfection mixture to the cells, (5) incubating the cells for 3 days, and (6) assaying integration of the exogenous sequence into a target locus (e.g., rDNA) in the cell genome, e.g., wherein one or more of the preceding steps are performed as described in Example 6 herein.

In some embodiments, the GENE WRITER™ polypeptide results in insertion of the heterologous object sequence (e.g., the GFP gene) into the target locus (e.g., rDNA) at an average copy number of at least 0.01, 0.025, 0.05, 0.075, 0.1, 0.15, 0.2, 0.25, 0.3, 0.4, 0.5, 0.75, 1, 1.25, 1.5, 1.75, 2, 2.5, 3, 4, or 5 copies per genome. In some embodiments, a cell described herein (e.g., a cell comprising a heterologous sequence at a target insertion site) comprises the heterologous object sequence at an average copy number of at least 0.01, 0.025, 0.05, 0.075, 0.1, 0.15, 0.2, 0.25, 0.3, 0.4, 0.5, 0.75, 1, 1.25, 1.5, 1.75, 2, 2.5, 3, 4, or 5 copies per genome. In some embodiments, a GENE WRITER™ causes integration of a sequence in a target RNA with relatively few truncation events at the terminus. For instance, in some embodiments, a GENE WRITER™ protein (e.g., of SEQ ID NO: 1016) results in about 25-100%, 50-100%, 60-100%, 70-100%, 75-95%, 80%-90%, or 86.17% of integrants into the target site being non-truncated, as measured by an assay described herein, e.g., an assay of Example 6 and FIG. 8. In some embodiments, a GENE WRITER™ protein (e.g., of SEQ ID NO: 1016) results in at least about 30%, 40%, 50%, 60%, 70%, 80%, or 90% of integrants into the target site being non-truncated, as measured by an assay described herein. In some embodiments, an integrant is classified as truncated versus non-truncated using an assay comprising amplification with a forward primer situated 565 bp from the end of the element (e.g., a wild-type transposon sequence, e.g., of Taeniopygia guttata) and a reverse primer situated in the genomic DNA of the target insertion site, e.g., rDNA. In some embodiments, the number of full-length integrants in the target insertion site is greater than the number of integrants truncated by 300-565 nucleotides in the target insertion site, e.g., the number of full-length integrants is at least 1.1×, 1.2×, 1.5×, 2×, 3×, 4×, 5×, 6×, 7×, 8×, 9×, or 10× the number of the truncated integrants, or the number of full-length integrants is at least 1.1×-10×, 2×-10×, 3×-10×, or 5×-10× the number of the truncated integrants.

In some embodiments, a system or method described herein results in insertion of the heterologous object sequence only at one target site in the genome of the target cell. Insertion can be measured, e.g., using a threshold of above 1%, 1.5%, 2%, 2.5%, 3%, 3.5%, 4%, 4.5%, 5%, e.g., as described in Example 8. In some embodiments, a system or method described herein results in insertion of the heterologous object sequence wherein less than 1%, 1.5%, 2%, 2.5%, 3%, 3.5%, 4%, 4.5%, 5%, 10%, 20%, 30%, 40%, or 50% of insertions are at a site other than the target site, e.g., using an assay described herein, e.g., an assay of Example 8.

In some embodiments, a system or method described herein results in “scarless” insertion of the heterologous object sequence, while in some embodiments, the target site can show deletions or duplications of endogenous DNA as a result of insertion of the heterologous sequence. The mechanisms of different retrotransposons could result in different patterns of duplications or deletions in the host genome occurring during retrotransposition at the target site. In some embodiments, the system results in a scarless insertion, with no duplications or deletions in the surrounding genomic DNA. In some embodiments, the system results in a deletion of less than 1, 2, 3, 4, 5, 10, 50, or 100 bp of genomic DNA upstream of the insertion. In some embodiments, the system results in a deletion of less than 1, 2, 3, 4, 5, 10, 50, or 100 bp of genomic DNA downstream of the insertion. In some embodiments, the system results in a duplication of less than 1, 2, 3, 4, 5, 10, 50, or 100 bp of genomic DNA upstream of the insertion. In some embodiments, the system results in a duplication of less than 1, 2, 3, 4, 5, 10, 50, or 100 bp of genomic DNA downstream of the insertion.

In some embodiments, a GENE WRITER™ described herein, or a DNA-binding domain thereof, binds to its target site specifically, e.g., as measured using an assay of Example 21. In some embodiments, the GENE WRITER™ or DNA-binding domain thereof binds to its target site more strongly than to any other binding site in the human genome. For example, in some embodiments, in an assay of Example 21, the target site represents more than 50%, 60%, 70%, 80%, 90%, or 95% of binding events of the GENE WRITER™ or DNA-binding domain thereof to human genomic DNA.

Genetically Engineered, e.g., Dimerized GENE WRITERT Genome Editor Polypeptides

Some non-LTR retrotransposons utilize two subunits to complete retrotransposition (Christensen et al PNAS 2006). In some embodiments, a retrotransposase described herein comprises two connected subunits as a single polypeptide. For instance, two wild-type retrotransposases could be joined with a linker to form a covalently “dimerized” protein (see FIG. 17). In some embodiments, the nucleic acid coding for the retrotransposase codes for two retrotransposase subunits to be expressed as a single polypeptide. In some embodiments, the subunits are connected by a peptide linker, such as has been described herein in the section entitled “Linker” and, e.g., in Chen et al Adv Drug Deliv Rev 2013. In some embodiments, the two subunits in the polypeptide are connected by a rigid linker. In some embodiments, the rigid linker consists of the motif (EAAAK)_n (SEQ ID NO: 1534). In other embodiments, the two subunits in the polypeptide are connected by a flexible linker. In some embodiments, the flexible linker consists of the motif (Gly)_n. In some embodiments, the flexible linker consists of the motif (GGGGS)_n (SEQ ID NO: 1535). In some embodiments, the rigid or flexible linker consists of 1, 2, 3, 4, 5, 10, 15, or more amino acids in length to enable retrotransposition. In some embodiments, the linker consists of a combination of rigid and flexible linker motifs.

Based on mechanism, not all functions are required from both retrotransposase subunits. In some embodiments, the fusion protein may consist of a fully functional subunit and a second subunit lacking one or more functional domains. In some embodiments, one subunit may lack reverse transcriptase functionality. In some embodiments, one subunit may lack the reverse transcriptase domain. In some embodiments, one subunit may possess only endonuclease activity. In some embodiments, one subunit may possess only an endonuclease domain. In some embodiments, the two subunits comprising the single polypeptide may provide complimentary functions.

In some embodiments, one subunit may lack endonuclease functionality. In some embodiments, one subunit may lack the endonuclease domain. In some embodiments, one subunit may possess only reverse transcriptase activity. In some embodiments, one subunit may possess only a reverse transcriptase domain. In some embodiments, one subunit may possess only DNA-dependent DNA synthesis functionality.

Linkers:

In some embodiments, domains of the compositions and systems described herein (e.g., the endonuclease and reverse transcriptase domains of a polypeptide or the DNA binding domain and reverse transcriptase domains of a polypeptide) may be joined by a linker. A composition described herein comprising a linker element has the general form S1-L-S2, wherein S1 and S2 may be the same or different and represent two domain moieties (e.g., each a polypeptide or nucleic acid domain) associated with one another by the linker. In some embodiments, a linker may connect two polypeptides. In some embodiments, a linker may connect two nucleic acid molecules. In some embodiments, a linker may connect a polypeptide and a nucleic acid molecule. A linker may be a chemical bond, e.g., one or more covalent bonds or non-covalent bonds. A linker may be flexible, rigid, and/or cleavable. In some embodiments, the linker is a peptide linker. Generally, a peptide linker is at least 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acids in length, e.g., 2-50 amino acids in length, 2-30 amino acids in length.

The most commonly used flexible linkers have sequences consisting primarily of stretches of Gly and Ser residues (“GS” linker). Flexible linkers may be useful for joining domains that require a certain degree of movement or interaction and may include small, non-polar (e.g. Gly) or polar (e.g. Ser or Thr) amino acids. Incorporation of Ser or Thr can also maintain the stability of the linker in aqueous solutions by forming hydrogen bonds with the water molecules, and therefore reduce unfavorable interactions between the linker and the other moieties. Examples of such linkers include those having the structure [GGS]^≥1 or [GGGS]^≥1 (SEQ ID NO: 1536). Rigid linkers are useful to keep a fixed distance between domains and to maintain their independent functions. Rigid linkers may also be useful when a spatial separation of the domains is critical to preserve the stability or bioactivity of one or more components in the agent. Rigid linkers may have an alpha helix-structure or Pro-rich sequence, (XP)n, with X designating any amino acid, preferably Ala, Lys, or Glu. Cleavable linkers may release free functional domains in vivo. In some embodiments, linkers may be cleaved under specific conditions, such as the presence of reducing reagents or proteases. In vivo cleavable linkers may utilize the reversible nature of a disulfide bond. One example includes a thrombin-sensitive sequence (e.g., PRS) between the two Cys residues. In vitro thrombin treatment of CPRSC (SEQ ID NO: 1537) results in the cleavage of the thrombin-sensitive sequence, while the reversible disulfide linkage remains intact. Such linkers are known and described, e.g., in Chen et al. 2013. Fusion Protein Linkers: Property, Design and Functionality. Adv Drug Deliv Rev. 65(10): 1357-1369. In vivo cleavage of linkers in compositions described herein may also be carried out by proteases that are expressed in vivo under pathological conditions (e.g. cancer or inflammation), in specific cells or tissues, or constrained within certain cellular compartments. The specificity of many proteases offers slower cleavage of the linker in constrained compartments.

In some embodiments the amino acid linkers are (or are homologous to) the endogenous amino acids that exist between such domains in a native polypeptide. In some embodiments the endogenous amino acids that exist between such domains are substituted but the length is unchanged from the natural length. In some embodiments, additional amino acid residues are added to the naturally existing amino acid residues between domains.

In some embodiments, the amino acid linkers are designed computationally or screened to maximize protein function (Anad et al., FEBS Letters, 587:19, 2013).

Template RNA Component of GENE WRITER™ Gene Editor System

TheGENE WRITER™ systems described herein can transcribe an RNA sequence template into host target DNA sites by target-primed reverse transcription. By writing DNA sequence(s) via reverse transcription of the RNA sequence template directly into the host genome, the GENE WRITER™ system can insert an object sequence into a target genome without the need for exogenous DNA sequences to be introduced into the host cell (unlike, for example, CRISPR systems), as well as eliminate an exogenous DNA insertion step. Therefore, the GENE WRITER™ system provides a platform for the use of customized RNA sequence templates containing object sequences, e.g., sequences comprising heterologous gene coding and/or function information.

In some embodiments the template RNA encodes a GENE WRITER™ protein in cis with a heterologous object sequence. Various cis constructs were described, for example, in Kuroki-Kami et al (2019) Mobile DNA 10:23 (incorporated by reference herein in its entirety), and can be used in combination with any of the embodiments described herein. For instance, in some embodiments, the template RNA comprises a heterologous object sequence, a sequence encoding a GENE WRITER™ protein (e.g., a protein comprising (i) a reverse transcriptase domain and (ii) an endonuclease domain, e.g., as described herein), a 5′ untranslated region, and a 3′ untranslated region. The components may be included in various orders. In some embodiments, the GENE WRITER™ protein and heterologous object sequence are encoded in different directions (sense vs. anti-sense), e.g., using an arrangement shown in FIG. 3A of Kuroki-Kami et al, Id. In some embodiments the GENE WRITER™ protein and heterologous object sequence are encoded in the same direction. In some embodiments, the nucleic acid encoding the polypeptide and the template RNA or the nucleic acid encoding the template RNA are covalently linked, e.g., are part of a fusion nucleic acid and/or are part of the same transcript. In some embodiments, the fusion nucleic acid comprises RNA or DNA.

The nucleic acid encoding the GENE WRITER™ polypeptide may, in some instances, be 5′ of the heterologous object sequence. For example, in some embodiments, the template RNA comprises, from 5′ to 3′, a 5′ untranslated region, a sense-encoded GENE WRITER™ polypeptide, a sense-encoded heterologous object sequence, and 3′ untranslated region. In some embodiments, the template RNA comprises, from 5′ to 3′, a 5′ untranslated region, a sense-encoded GENE WRITER™ polypeptide, anti-sense-encoded heterologous object sequence, and 3′ untranslated region.

In some embodiments, the RNA further comprises homology to the DNA target site.

It is understood that, when a template RNA is described as comprising an open reading frame or the reverse complement thereof, in some embodiments the template RNA must be converted into double stranded DNA (e.g., through reverse transcription) before the open reading frame can be transcribed and translated.

In certain embodiments, customized RNA sequence template can be identified, designed, engineered and constructed to contain sequences altering or specifying host genome function, for example by introducing a heterologous coding region into a genome; affecting or causing exon structure/alternative splicing; causing disruption of an endogenous gene; causing transcriptional activation of an endogenous gene; causing epigenetic regulation of an endogenous DNA; causing up- or down-regulation of operably liked genes, etc. In certain embodiments, a customized RNA sequence template can be engineered to contain sequences coding for exons and/or transgenes, provide for binding sites to transcription factor activators, repressors, enhancers, etc., and combinations of thereof. In other embodiments, the coding sequence can be further customized with splice acceptor sites, poly-A tails. In certain embodiments the RNA sequence can contain sequences coding for an RNA sequence template homologous to the RLE transposase, be engineered to contain heterologous coding sequences, or combinations thereof.

The template RNA may have some homology to the target DNA. In some embodiments the template RNA has at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 175, 200 or more bases of exact homology to the target DNA at the 3′ end of the RNA. In some embodiments the template RNA has at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 175, 180, or 200 or more bases of at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% homology to the target DNA, e.g., at the 5′ end of the template RNA. In some embodiments the template RNA has a 3′ untranslated region derived from a non-LTR retrotransposon, e.g. a non-LTR retrotransposons described herein. In some embodiments the template RNA has a 3′ region of at least 10, 15, 20, 25, 30, 40, 50, 60, 80, 100, 120, 140, 160, 180, 200 or more bases of at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% homology to the 3′ sequence of a non-LTR retrotransposon, e.g., a non-LTR retrotransposon described herein, e.g. a non-LTR retrotransposon in Table 1, 2, or 3. In some embodiments the template RNA has a 5′ untranslated region derived from a non-LTR retrotransposon, e.g. a non-LTR retrotransposons described herein. In some embodiments the template RNA has a 5′ region of at least 10, 15, 20, 25, 30, 40, 50, 60, 80, 100, 120, 140, 160, 180, or 200 or more bases of at least 40%, 50%, 60%, 70%, 80%, 90%, 95% or greater homology to the 5′ sequence of a non-LTR retrotransposon, e.g., a non-LTR retrotransposon described herein, e.g. a non-LTR retrotransposon described in Table 2 or 3.

The template RNA component of a GENE WRITER™ genome editing system described herein typically is able to bind the GENE WRITER™ genome editing protein of the system. In some embodiments the template RNA has a 3′ region that is capable of binding a GENE WRITER™ genome editing protein. The binding region, e.g., 3′ region, may be a structured RNA region, e.g., having at least 1, 2 or 3 hairpin loops, capable of binding the GENE WRITER™ genome editing protein of the system.

The template RNA component of a GENE WRITER™ genome editing system described herein typically is able to bind the GENE WRITER™ genome editing protein of the system. In some embodiments the template RNA has a 5′ region that is capable of binding a GENE WRITER™ genome editing protein. The binding region, e.g., 5′ region, may be a structured RNA region, e.g., having at least 1, 2 or 3 hairpin loops, capable of binding the GENE WRITER™ genome editing protein of the system. In some embodiments, the 5′ untranslated region comprises a pseudoknot, e.g., a pseudoknot that is capable of binding to the GENE WRITER™ protein.

In some embodiments, the template RNA (e.g., an untranslated region of the hairpin RNA, e.g., a 5′ untranslated region) comprises a stem-loop sequence. In some embodiments, the template RNA (e.g., an untranslated region of the hairpin RNA, e.g., a 5′ untranslated region) comprises a hairpin. In some embodiments, the template RNA (e.g., an untranslated region of the hairpin RNA, e.g., a 5′ untranslated region) comprises a helix. In some embodiments, the template RNA (e.g., an untranslated region of the hairpin RNA, e.g., a 5′ untranslated region) comprises a psuedoknot. In some embodiments the template RNA comprises a ribozyme. In some embodiments the ribozyme is similar to an hepatitis delta virus (HDV) ribozyme, e.g., has a secondary structure like that of the HDV ribozyme and/or has one or more activities of the HDV ribozyme, e.g., a self-cleavage activity. See, e.g., Eickbush et al., Molecular and Cellular Biology, 2010, 3142-3150.

In some embodiments, the template RNA (e.g., an untranslated region of the hairpin RNA, e.g., a 3′ untranslated region) comprises one or more stem-loops or helices. Exemplary structures of R2 3′ UTRs are shown, for example, in Ruschak et al. “Secondary structure models of the 3′ untranslated regions of diverse R2 RNAs” RNA. 2004 June; 10(6): 978-987, e.g., at FIG. 3, therein, and in Eikbush and Eikbush, “R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements” Mobile DNA (2012) 3:10; e.g., at FIG. 3 therein, which articles are hereby incorporated by reference in their entirety.

In some embodiments, a template RNA described herein comprises a sequence that is capable of binding to a GENE WRITER™ protein described herein. For instance, in some embodiments, the template RNA comprises an MS2 RNA sequence capable of binding to an MS2 coat protein sequence in the GENE WRITER™ protein. In some embodiments, the template RNA comprises an RNA sequence capable of binding to a B-box sequence. In some embodiments, the template RNA comprises an RNA sequence (e.g., a crRNA sequence and/or tracrRNA sequence) capable of binding to a dCas sequence in the GENE WRITER™ protein. In some embodiments, in addition to or in place of a UTR, the template RNA is linked (e.g., covalently) to a non-RNA UTR, e.g., a protein or small molecule.

In some embodiments the template RNA has a poly-A tail at the 3′ end. In some embodiments the template RNA does not have a poly-A tail at the 3′ end.

In some embodiments the template RNA has a 5′ region of at least 10, 15, 20, 25, 30, 40, 50, 60, 80, 100, 120, 140, 160, 180, 200 or more bases of at least 40%, 50%, 60%, 70%, 80%, 90%, 95% or greater homology to the 5′ sequence of a non-LTR retrotransposon, e.g., a non-LTR retrotransposon described herein.

The template RNA of the system typically comprises an object sequence for insertion into a target DNA. The object sequence may be coding or non-coding.

In some embodiments a system or method described herein comprises a single template RNA. In some embodiments a system or method described herein comprises a plurality of template RNAs.

In some embodiments, the object sequence may contain an open reading frame. In some embodiments the template RNA has a Kozak sequence. In some embodiments the template RNA has an internal ribosome entry site. In some embodiments the template RNA has a self-cleaving peptide such as a T2A or P2A site. In some embodiments the template RNA has a start codon. In some embodiments the template RNA has a splice acceptor site. In some embodiments the template RNA has a splice donor site. In some embodiments the template RNA has a microRNA binding site downstream of the stop codon. In some embodiments the template RNA has a polyA tail downstream of the stop codon of an open reading frame. In some embodiments the template RNA comprises one or more exons. In some embodiments the template RNA comprises one or more introns. In some embodiments the template RNA comprises a eukaryotic transcriptional terminator. In some embodiments the template RNA comprises an enhanced translation element or a translation enhancing element. In some embodiments the RNA comprises the human T-cell leukemia virus (HTLV-1) R region. In some embodiments the RNA comprises a posttranscriptional regulatory element that enhances nuclear export, such as that of Hepatitis B Virus (HPRE) or Woodchuck Hepatitis Virus (WPRE). In some embodiments, in the template RNA, the heterologous object sequence encodes a polypeptide and is coded in an antisense direction with respect to the 5′ and 3′ UTR. In some embodiments, in the template RNA, the heterologous object sequence encodes a polypeptide and is coded in a sense direction with respect to the 5′ and 3′ UTR.

In some embodiments, a nucleic acid described herein (e.g., a template RNA or a DNA encoding a template RNA) comprises a microRNA binding site. In some embodiments, the microRNA binding site is used to increase the target-cell specificity of a GENE WRITER™ system. For instance, the microRNA binding site can be chosen on the basis that is is recognized by a miRNA that is present in a non-target cell type, but that is not present (or is present at a reduced level relative to the non-target cell) in a target cell type. Thus, when the template RNA is present in a non-target cell, it would be bound by the miRNA, and when the template RNA is present in a target cell, it would not be bound by the miRNA (or bound but at reduced levels relative to the non-target cell). While not wishing to be bound by theory, binding of the miRNA to the template RNA may interfere with insertion of the heterologous object sequence into the genome. Accordingly, the heterologous object sequence would be inserted into the genome of target cells more efficiently than into the genome of non-target cells. A system having a microRNA binding site in the template RNA (or DNA encoding it) may also be used in combination with a nucleic acid encoding a GENE WRITER™ polypeptide, wherein expression of the GENE WRITER™ polypeptide is regulated by a second microRNA binding site, e.g., as described herein, e.g., in the section entitled “Polypeptide component of GENE WRITER™ gene editor system”.

In some embodiments, the object sequence may contain a non-coding sequence. For example, the template RNA may comprise a promoter or enhancer sequence. In some embodiments the template RNA comprises a tissue specific promoter or enhancer, each of which may be unidirectional or bidirectional. In some embodiments the promoter is an RNA polymerase I promoter, RNA polymerase II promoter, or RNA polymerase III promoter. In some embodiments the promoter comprises a TATA element. In some embodiments the promoter comprises a B recognition element. In some embodiments the promoter has one or more binding sites for transcription factors. In some embodiments the non-coding sequence is transcribed in an antisense-direction with respect to the 5′ and 3′ UTR. In some the non-coding sequence is transcribed in a sense direction with respect to the 5′ and 3′ UTR.

In some embodiments, a nucleic acid described herein (e.g., a template RNA or a DNA encoding a template RNA) comprises a promoter sequence, e.g., a tissue specific promoter sequence. In some embodiments, the tissue-specific promoter is used to increase the target-cell specificity of a GENE WRITER™ system. For instance, the promoter can be chosen on the basis that it is active in a target cell type but not active in (or active at a lower level in) a non-target cell type. Thus, even if the promoter integrated into the genome of a non-target cell, it would not drive expression (or only drive low level expression) of an integrated gene. A system having a tissue-specific promoter sequence in the template RNA may also be used in combination with a microRNA binding site, e.g., in the template RNA or a nucleic acid encoding a GENE WRITER™ protein, e.g., as described herein. A system having a tissue-specific promoter sequence in the template RNA may also be used in combination with a DNA encoding a GENE WRITER™ polypeptide, driven by a tissue-specific promoter, e.g., to achieve higher levels of GENE WRITER™ protein in target cells than in non-target cells.

In some embodiments the template RNA comprises a microRNA sequence, a siRNA sequence, a guide RNA sequence, a piwi RNA sequence.

In some embodiments the template RNA comprises a site that coordinates epigenetic modification. In some embodiments the template RNA comprises an element that inhibits, e.g., prevents, epigenetic silencing. In some embodiments the template RNA comprises a chromatin insulator. For example, the template RNA comprises a CTCF site or a site targeted for DNA methylation.

In order to promote higher level or more stable gene expression, the template RNA may include features that prevent or inhibit gene silencing. In some embodiments, these features prevent or inhibit DNA methylation. In some embodiments, these features promote DNA demethylation. In some embodiments, these features prevent or inhibit histone deacetylation. In some embodiments, these features prevent or inhibit histone methylation. In some embodiments, these features promote histone acetylation. In some embodiments, these features promote histone demethylation. In some embodiments, multiple features may be incorporated into the template RNA to promote one or more of these modifications. CpG dinculeotides are subject to methylation by host methyl transferases. In some embodiments, the template RNA is depleted of CpG dinucleotides, e.g., does not comprise CpG nucleotides or comprises a reduced number of CpG dinucleotides compared to a corresponding unaltered sequence. In some embodiments, the promoter driving transgene expression from integrated DNA is depleted of CpG dinucleotides.

In some embodiments the template RNA comprises a gene expression unit composed of at least one regulatory region operably linked to an effector sequence. The effector sequence may be a sequence that is transcribed into RNA (e.g., a coding sequence or a non-coding sequence such as a sequence encoding a micro RNA).

In some embodiments the object sequence of the template RNA is inserted into a target genome in an endogenous intron. In some embodiments the object sequence of the template RNA is inserted into a target genome and thereby acts as a new exon. In some embodiments the insertion of the object sequence into the target genome results in replacement of a natural exon or the skipping of a natural exon.

In some embodiments the object sequence of the template RNA is inserted into the target genome in a genomic safe harbor site, such as AAVS1, CCR5, or ROSA26. In some embodiment the object sequence of the template RNA is added to the genome in an intergenic or intragenic region. In some embodiments the object sequence of the template RNA is added to the genome 5′ or 3′ within 0.1 kb, 0.25 kb, 0.5 kb, 0.75, kb, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 7.5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 50, 75 kb, or 100 kb of an endogenous active gene. In some embodiments the object sequence of the template RNA is added to the genome 5′ or 3′ within 0.1 kb, 0.25 kb, 0.5 kb, 0.75, kb, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 7.5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 50, 75 kb, or 100 kb of an endogenous promoter or enhancer. In some embodiments the object sequence of the template RNA can be, e.g., 50-50,000 base pairs (e.g., between 50-40,000 bp, between 500-30,000 bp between 500-20,000 bp, between 100-15,000 bp, between 500-10,000 bp, between 50-10,000 bp, between 50-5,000 bp. In some embodiments, the heterologous object sequence is less than 1,000, 1,300, 1500, 2,000, 3,000, 4,000, 5,000, or 7,500 nucleotides in length.

In some embodiments the genomic safe harbor site is a NATURAL HARBOR™ site. In some embodiments the NATURAL HARBOR™ site is ribosomal DNA (rDNA). In some embodiments the NATURAL HARBOR™ site is 5S rDNA, 18S rDNA, 5.8S rDNA, or 28S rDNA. In some embodiments the NATURAL HARBOR™ site is the Mutsu site in 5S rDNA. In some embodiments the NATURAL HARBOR™ site is the R2 site, the R5 site, the R6 site, the R4 site, the R1 site, the R9 site, or the RT site in 28S rDNA. In some embodiments the NATURAL HARBOR™ site is the R8 site or the R7 site in 18S rDNA. In some embodiments the NATURAL HARBOR™ site is DNA encoding transfer RNA (tRNA). In some embodiments the NATURAL HARBOR™ site is DNA encoding tRNA-Asp or tRNA-Glu. In some embodiments the NATURAL HARBOR™ site is DNA encoding spliceosomal RNA. In some embodiments the NATURAL HARBOR™ site is DNA encoding small nuclear RNA (snRNA) such as U2 snRNA.

Thus, in some aspects, the present disclosure provides a method of inserting a heterologous object sequence into a NATURAL HARBOR™ site. In some embodimetns, the method comprises using a GENE WRITER™ system described herein, e.g., using a polypeptide of any of Tables 1-3 or a polypeptide having sequence similarity thereto, e.g., at least 80%, 85%, 90%, or 95% identity thereto. In some embodiments, the method comprises using an enzyme, e.g., a retrotransposase, to insert the heterologous object sequence into the NATURAL HARBOR™ site. In some aspects, the present disclosure provides a host human cell comprising a heterologous object sequence (e.g., a sequence encoding a therapeutic polypeptide) situated at a NATURAL HARBOR™ site in the genome of the cell. In some embodiments, the NATURAL HARBOR™ site is a site described in Table 4 below. In some embodiments, the heterologous object sequence is inserted within 20, 50, 100, 150, 200, 250, 500, or 1000 base pairs of a sequence shown in Table 4. In some embodiments, the heterologous object sequence is inserted within 0.1 kb, 0.25 kb, 0.5 kb, 0.75, kb, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 7.5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 50, 75 kb, or 100 kb of a sequence shown in Table 4. In some embodiments, the heterologous object sequence is inserted into a site having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to a sequence shown in Table 4. In some embodiments, the heterologous object sequence is inserted within 20, 50, 100, 150, 200, 250, 500, or 1000 base pairs, or within 0.1 kb, 0.25 kb, 0.5 kb, 0.75, kb, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 7.5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 50, 75 kb, or 100 kb, of a site having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to a sequence shown in Table 4. In some embodiments, the heterologous object sequence is inserted within a gene indicated in Column 5 of Table 4, or within 20, 50, 100, 150, 200, 250, 500, or 1000 base pairs, or within 0.1 kb, 0.25 kb, 0.5 kb, 0.75, kb, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 7.5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 50, 75 kb, or 100 kb, of the gene.

TABLE 4
NATURAL HARBOR ™ sites.
Column 1 indicates a retrotransposon that
inserts into the NATURAL HARBOR ™ site. Column 2 indicates the gene at the NATURAL
HARBOR ™ site. Columns 3 and 4 show exemplary human genome sequence 5′ and 3′ of the
insertion site (for example, 250 bp). Columns 5 and 6 list the example gene symbol and
corresponding Gene ID.
				Example
Target	Target			Gene	Example
Site	Gene	5′ flanking sequence	3′ flanking sequence	Symbol	Gene ID
R2	28S rDNA	CCGGTCCCCCCCGCCGGGTCC	GTAGCCAAATGCCTCGTCATC	RNA28SN1	106632264
		GCCCCCGGGGCCGCGGTTCC	TAATTAGTGACGCGCATGAAT
		GCGCGGCGCCTCGCCTCGGC	GGATGAACGAGATTCCCACT
		CGGCGCCTAGCAGCCGACTT	GTCCCTACCTACTATCCAGCG
		AGAACTGGTGCGGACCAGGG	AAACCACAGCCAAGGGAACG
		GAATCCGACTGTTTAATTAAA	GGCTTGGCGGAATCAGCGGG
		ACAAAGCATCGCGAAGGCCC	GAAAGAAGACCCTGTTGAGC
		GCGGCGGGTGTTGACGCGAT	TTGACTCTAGTCTGGCACGGT
		GTGATTTCTGCCCAGTGCTCT	GAAGAGACATGAGAGGTGTA
		GAATGTCAAAGTGAAGAAAT	GAATAAGTGGGAGGCCCCCG
		TCAATGAAGCGCGGGTAAAC	GCGCCCCCCCGGTGTCCCCGC
		GGCGGGAGTAACTATGACTC	GAGGGGCCCGGGGCGGGGT
		TCTTAAG (SEQ ID NO: 1508)	CCGCCG (SEQ ID NO: 1513)
R4	28S rDNA	GCGGTTCCGCGCGGCGCCTC	CGCATGAATGGATGAACGAG	RNA28SN1	106632264
		GCCTCGGCCGGCGCCTAGCA	ATTCCCACTGTCCCTACCTACT
		GCCGACTTAGAACTGGTGCG	ATCCAGCGAAACCACAGCCA
		GACCAGGGGAATCCGACTGT	AGGGAACGGGCTTGGCGGA
		TTAATTAAAACAAAGCATCGC	ATCAGCGGGGAAAGAAGACC
		GAAGGCCCGCGGCGGGTGTT	CTGTTGAGCTTGACTCTAGTC
		GACGCGATGTGATTTCTGCCC	TGGCACGGTGAAGAGACATG
		AGTGCTCTGAATGTCAAAGT	AGAGGTGTAGAATAAGTGGG
		GAAGAAATTCAATGAAGCGC	AGGCCCCCGGCGCCCCCCCG
		GGGTAAACGGCGGGAGTAAC	GTGTCCCCGCGAGGGGCCCG
		TATGACTCTCTTAAGGTAGCC	GGGCGGGGTCCGCCGGCCCT
		AAATGCCTCGTCATCTAATTA	GCGGGCCGCCGGTGAAATAC
		GTGACG (SEQ ID NO: 1509)	CACTACTC (SEQ ID NO:
			1514)
R5	28S rDNA	TCCCCCCCGCCGGGTCCGCCC	CCAAATGCCTCGTCATCTAAT	RNA28SN1	106632264
		CCGGGGCCGCGGTTCCGCGC	TAGTGACGCGCATGAATGGA
		GGCGCCTCGCCTCGGCCGGC	TGAACGAGATTCCCACTGTCC
		GCCTAGCAGCCGACTTAGAA	CTACCTACTATCCAGCGAAAC
		CTGGTGCGGACCAGGGGAAT	CACAGCCAAGGGAACGGGCT
		CCGACTGTTTAATTAAAACAA	TGGCGGAATCAGCGGGGAAA
		AGCATCGCGAAGGCCCGCGG	GAAGACCCTGTTGAGCTTGA
		CGGGTGTTGACGCGATGTGA	CTCTAGTCTGGCACGGTGAA
		TTTCTGCCCAGTGCTCTGAAT	GAGACATGAGAGGTGTAGAA
		GTCAAAGTGAAGAAATTCAA	TAAGTGGGAGGCCCCCGGCG
		TGAAGCGCGGGTAAACGGCG	CCCCCCCGGTGTCCCCGCGAG
		GGAGTAACTATGACTCTCTTA	GGGCCCGGGGCGGGGTCCG
		AGGTAG (SEQ ID NO: 1510)	CCGGCCC (SEQ ID NO: 1515)
R9	28S rDNA	CGGCGCGCTCGCCGGCCGAG	TAGCTGGTTCCCTCCGAAGTT	RNA28SN1	106632264
		GTGGGATCCCGAGGCCTCTC	TCCCTCAGGATAGCTGGCGCT
		CAGTCCGCCGAGGGCGCACC	CTCGCAGACCCGACGCACCCC
		ACCGGCCCGTCTCGCCCGCCG	CGCCACGCAGTTTTATCCGGT
		CGCCGGGGAGGTGGAGCAC	AAAGCGAATGATTAGAGGTC
		GAGCGCACGTGTTAGGACCC	TTGGGGCCGAAACGATCTCA
		GAAAGATGGTGAACTATGCC	ACCTATTCTCAAACTTTAAAT
		TGGGCAGGGCGAAGCCAGA	GGGTAAGAAGCCCGGCTCGC
		GGAAACTCTGGTGGAGGTCC	TGGCGTGGAGCCGGGCGTGG
		GTAGCGGTCCTGACGTGCAA	AATGCGAGTGCCTAGTGGGC
		ATCGGTCGTCCGACCTGGGT	CACTTTTGGTAAGCAGAACTG
		ATAGGGGCGAAAGACTAATC	GCGCTGCGGGATGAACCGAA
		GAACCATCTAG (SEQ ID NO:	CGCC (SEQ ID NO: 1516)
		1511)
R8	18S rDNA	GCATTCGTATTGCGCCGCTAG	TGAAACTTAAAGGAATTGAC	RNA18SN1	106631781
		AGGTGAAATTCTTGGACCGG	GGAAGGGCACCACCAGGAGT
		CGCAAGACGGACCAGAGCGA	GGAGCCTGCGGCTTAATTTG
		AAGCATTTGCCAAGAATGTTT	ACTCAACACGGGAAACCTCA
		TCATTAATCAAGAACGAAAGT	CCCGGCCCGGACACGGACAG
		CGGAGGTTCGAAGACGATCA	GATTGACAGATTGATAGCTCT
		GATACCGTCGTAGTTCCGACC	TTCTCGATTCCGTGGGTGGTG
		ATAAACGATGCCGACCGGCG	GTGCATGGCCGTTCTTAGTTG
		ATGCGGCGGCGTTATTCCCAT	GTGGAGCGATTTGTCTGGTT
		GACCCGCCGGGCAGCTTCCG	AATTCCGATAACGAACGAGA
		GGAAACCAAAGTCTTTGGGT	CTCTGGCATGCTAACTAGTTA
		TCCGGGGGGAGTATGGTTGC	CGCGACCCCCGAGCGGTCGG
		AAAGC (SEQ ID NO: 1512)	CGTCCC (SEQ ID NO: 1517)
R4-	tRNA-Asp			TRD-GTC1-1	100189207
2_SRa
LIN25_	tRNA-Glu			TRE-CTC1-1	100189384
SM
R1	28S rDNA	TAGCAGCCGACTTAGAACTG	ACCTACTATCCAGCGAAACCA	RNA28SN1	106632264
		GTGCGGACCAGGGGAATCCG	CAGCCAAGGGAACGGGCTTG
		ACTGTTTAATTAAAACAAAGC	GCGGAATCAGCGGGGAAAG
		ATCGCGAAGGCCCGCGGCGG	AAGACCCTGTTGAGCTTGACT
		GTGTTGACGCGATGTGATTTC	CTAGTCTGGCACGGTGAAGA
		TGCCCAGTGCTCTGAATGTCA	GACATGAGAGGTGTAGAATA
		AAGTGAAGAAATTCAATGAA	AGTGGGAGGCCCCCGGCGCC
		GCGCGGGTAAACGGCGGGA	CCCCCGGTGTCCCCGCGAGG
		GTAACTATGACTCTCTTAAGG	GGCCCGGGGCGGGGTCCGCC
		TAGCCAAATGCCTCGTCATCT	GGCCCTGCGGGCCGCCGGTG
		AATTAGTGACGCGCATGAAT	AAATACCACTACTCTGATCGT
		GGATGAACGAGATTCCCACT	TTTTTCACTGACCCGGTGAGG
		GTCCCT (SEQ ID NO: 1518)	CGGGGGG (SEQ ID NO:
			1524)
R6	28S rDNA	CCCCCCGCCGGGTCCGCCCCC	AAATGCCTCGTCATCTAATTA	RNA28SN1	106632264
		GGGGCCGCGGTTCCGCGCGG	GTGACGCGCATGAATGGATG
		CGCCTCGCCTCGGCCGGCGC	AACGAGATTCCCACTGTCCCT
		CTAGCAGCCGACTTAGAACT	ACCTACTATCCAGCGAAACCA
		GGTGCGGACCAGGGGAATCC	CAGCCAAGGGAACGGGCTTG
		GACTGTTTAATTAAAACAAAG	GCGGAATCAGCGGGGAAAG
		CATCGCGAAGGCCCGCGGCG	AAGACCCTGTTGAGCTTGACT
		GGTGTTGACGCGATGTGATT	CTAGTCTGGCACGGTGAAGA
		TCTGCCCAGTGCTCTGAATGT	GACATGAGAGGTGTAGAATA
		CAAAGTGAAGAAATTCAATG	AGTGGGAGGCCCCCGGCGCC
		AAGCGCGGGTAAACGGCGG	CCCCCGGTGTCCCCGCGAGG
		GAGTAACTATGACTCTCTTAA	GGCCCGGGGCGGGGTCCGCC
		GGTAGCC (SEQ ID NO: 1519)	GGCCCTG (SEQ ID NO: 1525)
R7	18S rDNA	GCGCAAGACGGACCAGAGCG	GGAGCCTGCGGCTTAATTTG	RNA18SN1	106631781
		AAAGCATTTGCCAAGAATGTT	ACTCAACACGGGAAACCTCA
		TTCATTAATCAAGAACGAAAG	CCCGGCCCGGACACGGACAG
		TCGGAGGTTCGAAGACGATC	GATTGACAGATTGATAGCTCT
		AGATACCGTCGTAGTTCCGAC	TTCTCGATTCCGTGGGTGGTG
		CATAAACGATGCCGACCGGC	GTGCATGGCCGTTCTTAGTTG
		GATGCGGCGGCGTTATTCCC	GTGGAGCGATTTGTCTGGTT
		ATGACCCGCCGGGCAGCTTC	AATTCCGATAACGAACGAGA
		CGGGAAACCAAAGTCTTTGG	CTCTGGCATGCTAACTAGTTA
		GTTCCGGGGGGAGTATGGTT	CGCGACCCCCGAGCGGTCGG
		GCAAAGCTGAAACTTAAAGG	CGTCCCCCAACTTCTTAGAGG
		AATTGACGGAAGGGCACCAC	GACAAGTGGCGTTCAGCCAC
		CAGGAGT (SEQ ID NO: 1520)	CCGAG (SEQ ID NO: 1526)
RT	28S rDNA	GGCCGGGCGCGACCCGCTCC	AACTGGCTTGTGGCGGCCAA	RNA28SN1	106632264
		GGGGACAGTGCCAGGTGGG	GCGTTCATAGCGACGTCGCTT
		GAGTTTGACTGGGGCGGTAC	TTTGATCCTTCGATGTCGGCT
		ACCTGTCAAACGGTAACGCA	CTTCCTATCATTGTGAAGCAG
		GGTGTCCTAAGGCGAGCTCA	AATTCACCAAGCGTTGGATTG
		GGGAGGACAGAAACCTCCCG	TTCACCCACTAATAGGGAACG
		TGGAGCAGAAGGGCAAAAG	TGAGCTGGGTTTAGACCGTC
		CTCGCTTGATCTTGATTTTCA	GTGAGACAGGTTAGTTTTACC
		GTACGAATACAGACCGTGAA	CTACTGATGATGTGTTGTTGC
		AGCGGGGCCTCACGATCCTTC	CATGGTAATCCTGCTCAGTAC
		TGACCTTTTGGGTTTTAAGCA	GAGAGGAACCGCAGGTTCAG
		GGAGGTGTCAGAAAAGTTAC	ACATTTGGTGTATGTGCTTGG
		CACAGGGAT (SEQ ID NO:	C (SEQ ID NO: 1527)
		1521)
Mutsu	5S rDNA	GTCTACGGCCATACCACCC	TGAACGCGCCCGATCTCGTCT	RNA5S1	100169751
		(SEQ ID NO: 1522)	GATCTCGGAAGCTAAGCAGG
			GTCGGGCCTGGTTAGTACTT
			GGATGGGAGACCGCCTGGGA
			ATACCGGGTGCTGTAGGCTTT
			(SEQ ID NO: 1528)
Utopia/	U2 snRNA	ATCGCTTCTCGGCCTTTTGGC	TCTGTTCTTATCAGTTTAATAT	RNU2-1	6066
Keno		TAAGATCAAGTGTAGTA (SEQ	CTGATACGTCCTCTATCCGAG
		ID NO: 1523)	GACAATATATTAAATGGATTT
			TTGGAGCAGGGAGATGGAAT
			AGGAGCTTGCTCCGTCCACTC
			CACGCATCGACCTGGTATTGC
			AGTACCTCCAGGAACGGTGC
			ACCC (SEQ ID NO: 1529)

In some embodiments, a system or method described herein results in insertion of a heterologous sequence into a target site in the human genome. In some embodiments, the target site in the human genome has sequence similarity to the corresponding target site of the corresponding wild-type retrotransposase (e.g., the retrotransposase from which the GENE WRITER™ was derived) in the genome of the organism to which it is native. For instance, in some embodiments, the identity between the 40 nucleotides of human genome sequence centered at the insertion site and the 40 nucleotides of native organism genome sequence centered at the insertion site is less than 99.5%, 99%, 98%, 97%, 96%, 95%, 90%, 85%, 80%, 75%, 70%, 60%, or 50%, or is between 50-60%, 60-70%, 70-80%, 80-90%, or 90-100%. In some embodiments, the identity between the 100 nucleotides of human genome sequence centered at the insertion site and the 100 nucleotides of native organism genome sequence centered at the insertion site is less than 99.5%, 99%, 98%, 97%, 96%, 95%, 90%, 85%, 80%, 75%, 70%, 60%, or 50%, or is between 50-60%, 60-70%, 70-80%, 80-90%, or 90-100%. In some embodiments, the identity between the 500 nucleotides of human genome sequence centered at the insertion site and the 500 nucleotides of native organism genome sequence centered at the insertion site is less than 99.5%, 99%, 98%, 97%, 96%, 95%, 90%, 85%, 80%, 75%, 70%, 60%, or 50%, or is between 50-60%, 60-70%, 70-80%, 80-90%, or 90-100%.

Production of Compositions and Systems

As will be appreciated by one of skill, methods of designing and constructing nucleic acid constructs and proteins or polypeptides (such as the systems, constructs and polypeptides described herein) are routine in the art. Generally, recombinant methods may be used. See, in general, Smales & James (Eds.), Therapeutic Proteins: Methods and Protocols (Methods in Molecular Biology), Humana Press (2005); and Crommelin, Sindelar & Meibohm (Eds.), Pharmaceutical Biotechnology: Fundamentals and Applications, Springer (2013). Methods of designing, preparing, evaluating, purifying and manipulating nucleic acid compositions are described in Green and Sambrook (Eds.), Molecular Cloning: A Laboratory Manual (Fourth Edition), Cold Spring Harbor Laboratory Press (2012).

Exemplary methods for producing a therapeutic pharmaceutical protein or polypeptide described herein involve expression in mammalian cells, although recombinant proteins can also be produced using insect cells, yeast, bacteria, or other cells under control of appropriate promoters. Mammalian expression vectors may comprise non-transcribed elements such as an origin of replication, a suitable promoter, and other 5′ or 3′ flanking non-transcribed sequences, and 5′ or 3′ non-translated sequences such as necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, and termination sequences. DNA sequences derived from the SV40 viral genome, for example, SV40 origin, early promoter, splice, and polyadenylation sites may be used to provide other genetic elements required for expression of a heterologous DNA sequence. Appropriate cloning and expression vectors for use with bacterial, fungal, yeast, and mammalian cellular hosts are described in Green & Sambrook, Molecular Cloning: A Laboratory Manual (Fourth Edition), Cold Spring Harbor Laboratory Press (2012).

Various mammalian cell culture systems can be employed to express and manufacture recombinant protein. Examples of mammalian expression systems include CHO, COS, HEK293, HeLA, and BHK cell lines. Processes of host cell culture for production of protein therapeutics are described in Zhou and Kantardjieff (Eds.), Mammalian Cell Cultures for Biologics Manufacturing (Advances in Biochemical Engineering/Biotechnology), Springer (2014). Compositions described herein may include a vector, such as a viral vector, e.g., a lentiviral vector, encoding a recombinant protein. In some embodiments, a vector, e.g., a viral vector, may comprise a nucleic acid encoding a recombinant protein.

Purification of protein therapeutics is described in Franks, Protein Biotechnology: Isolation, Characterization, and Stabilization, Humana Press (2013); and in Cutler, Protein Purification Protocols (Methods in Molecular Biology), Humana Press (2010).

Applications

By integrating coding genes into a RNA sequence template, the GENE WRITER™ system can address therapeutic needs, for example, by providing expression of a therapeutic transgene in individuals with loss-of-function mutations, by replacing gain-of-function mutations with normal transgenes, by providing regulatory sequences to eliminate gain-of-function mutation expression, and/or by controlling the expression of operably linked genes, transgenes and systems thereof. In certain embodiments, the RNA sequence template encodes a promotor region specific to the therapeutic needs of the host cell, for example a tissue specific promotor or enhancer. In still other embodiments, a promotor can be operably linked to a coding sequence.

In embodiments, the GENE WRITER™ gene editor system can provide therapeutic transgenes expressing, e.g., replacement blood factors or replacement enzymes, e.g., lysosomal enzymes. For example, the compositions, systems and methods described herein are useful to express, in a target human genome, agalsidase alpha or beta for treatment of Fabry Disease; imiglucerase, taliglucerase alfa, velaglucerase alfa, or alglucerase for Gaucher Disease; sebelipase alpha for lysosomal acid lipase deficiency (Wolman disease/CESD); laronidase, idursulfase, elosulfase alpha, or galsulfase for mucopolysaccharidoses; alglucosidase alpha for Pompe disease. For example, the compositions, systems and methods described herein are useful to express, in a target human genome factor I, II, V, VII, X, XI, XII or XIII for blood factor deficiencies.

In some embodiments, the heterologous object sequence encodes an intracellular protein (e.g., a cytoplasmic protein, a nuclear protein, an organellar protein such as a mitochondrial protein or lysosomal protein, or a membrane protein). In some embodiments, the heterologous object sequence encodes a membrane protein, e.g., a membrane protein other than a CAR, and/or an endogenous human membrane protein. In some embodiments, the heterologous object sequence encodes an extracellular protein. In some embodiments, the heterologous object sequence encodes an enzyme, a structural protein, a signaling protein, a regulatory protein, a transport protein, a sensory protein, a motor protein, a defense protein, or a storage protein.

Administration

The composition and systems described herein may be used in vitro or in vivo. In some embodiments the system or components of the system are delivered to cells (e.g., mammalian cells, e.g., human cells), e.g., in vitro or in vivo. In some embodiments, the cells are eukaryotic cells, e.g., cells of a multicellular organism, e.g., an animal, e.g., a mammal (e.g., human, swine, bovine) a bird (e.g., poultry, such as chicken, turkey, or duck), or a fish. In some embodiments, the cells are non-human animal cells (e.g., a laboratory animal, a livestock animal, or a companion animal). In some embodiments, the cell is a stem cell (e.g., a hematopoietic stem cell), a fibroblast, or a T cell. In some embodiments, the cell is a non-dividing cell, e.g., a non-dividing fibroblast or non-dividing T cell. In some embodiments, the cell is an HSC and p53 is not upregulated or is upregulated by less than 10%, 5%, 2%, or 1%, e.g., as determined according to the method described in Example 30. The skilled artisan will understand that the components of the GENE WRITER™ system may be delivered in the form of polypeptide, nucleic acid (e.g., DNA, RNA), and combinations thereof.

For instance, delivery can use any of the following combinations for delivering the retrotransposase (e.g., as DNA encoding the retrotransposase protein, as RNA encoding the retrotransposase protein, or as the protein itself) and the template RNA (e.g., as DNA encoding the RNA, or as RNA):

• • 1. Retrotransposase DNA+template DNA
  • 2. Retrotransposase RNA+template DNA
  • 3. Retrotransposase DNA+template RNA
  • 4. Retrotransposase RNA+template RNA
  • 5. Retrotransposase protein+template DNA
  • 6. Retrotransposase protein+template RNA
  • 7. Retrotransposase virus+template virus
  • 8. Retrotransposase virus+template DNA
  • 9. Retrotransposase virus+template RNA
  • 10. Retrotransposase DNA+template virus
  • 11. Retrotransposase RNA+template virus
  • 12. Retrotransposase protein+template virus

As indicated above, in some embodiments, the DNA or RNA that encodes the retrotransposase protein is delivered using a virus, and in some embodiments, the template RNA (or the DNA encoding the template RNA) is delivered using a virus.

In one embodiments the system and/or components of the system are delivered as nucleic acid. For example, the GENE WRITER™ polypeptide may be delivered in the form of a DNA or RNA encoding the polypeptide, and the template RNA may be delivered in the form of RNA or its complementary DNA to be transcribed into RNA. In some embodiments the system or components of the system are delivered on 1, 2, 3, 4, or more distinct nucleic acid molecules. In some embodiments the system or components of the system are delivered as a combination of DNA and RNA. In some embodiments the system or components of the system are delivered as a combination of DNA and protein. In some embodiments the system or components of the system are delivered as a combination of RNA and protein. In some embodiments the GENE WRITER™ genome editor polypeptide is delivered as a protein.

In some embodiments the system or components of the system are delivered to cells, e.g. mammalian cells or human cells, using a vector. The vector may be, e.g., a plasmid or a virus. In some embodiments delivery is in vivo, in vitro, ex vivo, or in situ. In some embodiments the virus is an adeno associated virus (AAV), a lentivirus, an adenovirus. In some embodiments the system or components of the system are delivered to cells with a viral-like particle or a virosome. In some embodiments the delivery uses more than one virus, viral-like particle or virosome.

In one embodiment, the compositions and systems described herein can be formulated in liposomes or other similar vesicles. Liposomes are spherical vesicle structures composed of a uni- or multilamellar lipid bilayer surrounding internal aqueous compartments and a relatively impermeable outer lipophilic phospholipid bilayer. Liposomes may be anionic, neutral or cationic. Liposomes are biocompatible, nontoxic, can deliver both hydrophilic and lipophilic drug molecules, protect their cargo from degradation by plasma enzymes, and transport their load across biological membranes and the blood brain barrier (BBB) (see, e.g., Spuch and Navarro, Journal of Drug Delivery, vol. 2011, Article ID 469679, 12 pages, 2011 for review).

Vesicles can be made from several different types of lipids; however, phospholipids are most commonly used to generate liposomes as drug carriers. Methods for preparation of multilamellar vesicle lipids are known in the art (see for example U.S. Pat. No. 6,693,086, the teachings of which relating to multilamellar vesicle lipid preparation are incorporated herein by reference). Although vesicle formation can be spontaneous when a lipid film is mixed with an aqueous solution, it can also be expedited by applying force in the form of shaking by using a homogenizer, sonicator, or an extrusion apparatus (see, e.g., Spuch and Navarro, Journal of Drug Delivery, vol. 2011, Article ID 469679, 12 pages, 2011 for review). Extruded lipids can be prepared by extruding through filters of decreasing size, as described in Templeton et al., Nature Biotech, 15:647-652, 1997, the teachings of which relating to extruded lipid preparation are incorporated herein by reference.

Lipid nanoparticles are another example of a carrier that provides a biocompatible and biodegradable delivery system for the pharmaceutical compositions described herein. Nanostructured lipid carriers (NLCs) are modified solid lipid nanoparticles (SLNs) that retain the characteristics of the SLN, improve drug stability and loading capacity, and prevent drug leakage. Polymer nanoparticles (PNPs) are an important component of drug delivery. These nanoparticles can effectively direct drug delivery to specific targets and improve drug stability and controlled drug release. Lipid-polymer nanoparticles (PLNs), a new type of carrier that combines liposomes and polymers, may also be employed. These nanoparticles possess the complementary advantages of PNPs and liposomes. A PLN is composed of a core-shell structure; the polymer core provides a stable structure, and the phospholipid shell offers good biocompatibility. As such, the two components increase the drug encapsulation efficiency rate, facilitate surface modification, and prevent leakage of water-soluble drugs. For a review, see, e.g., Li et al. 2017, Nanomaterials 7, 122.

Exosomes can also be used as drug delivery vehicles for the compositions and systems described herein. For a review, see Ha et al. July 2016. Acta Pharmaceutica Sinica B. Volume 6, Issue 4, Pages 287-296.

A GENE WRITER™ system can be introduced into cells, tissues and multicellular organisms. In some embodiments the system or components of the system are delivered to the cells via mechanical means or physical means.

Formulation of protein therapeutics is described in Meyer (Ed.), Therapeutic Protein Drug Products: Practical Approaches to formulation in the Laboratory, Manufacturing, and the Clinic, Woodhead Publishing Series (2012).

All publications, patent applications, patents, and other publications and references (e.g., sequence database reference numbers) cited herein are incorporated by reference in their entirety. For example, all GENBANK™, UNIGENE™, and ENTREZ™ sequences referred to herein, e.g., in any Table herein, are incorporated by reference. Unless otherwise specified, the sequence accession numbers specified herein, including in any Table herein, refer to the database entries current as of Aug. 27, 2018. When one gene or protein references a plurality of sequence accession numbers, all of the sequence variants are encompassed.

EXAMPLES

The invention is further illustrated by the following examples. The examples are provided for illustrative purposes only and are not to be construed as limiting the scope or content of the invention in any way.

Example 1: Delivery of a GENE WRITER™ System to Mammalian Cells

This example describes a GENE WRITER™ genome editing system delivered to a mammalian cell for site-specific insertion of exogenous DNA into a mammalian cell genome.

In this example, the polypeptide component of the GENE WRITER™ system is the R2Bm protein from Bombyx mori and the template RNA component is RNA for the R2Bm retrotransposase from Bombyx mori containing a mutation in the reverse transcriptase domain that renders the retrotransposase inactive.

HEK293T cells are transfected with the following test agents:

• • 1. Scrambled RNA control
  • 2. RNA coding for the polypeptide described above
  • 3. Template RNA described above
  • 4. Combination of 2 and 3

After transfection, HEK293T cells are cultured for at least 4 days and then assayed for site-specific genome editing. Genomic DNA is isolated from each group of HEK293 cells. PCR is conducted with primers that flank the R2Bm integration site in 28s rRNA genes. The PCR product is run on an agarose gel to measure the length of the amplified DNA.

A PCR product of the expected length, indicative of a successful GENE WRITING™ genome editing event that inserts the sequence for the mutated R2Bm retrotransposase into the target genome, is observed only in cells that were transfected with the complete GENE WRITER™ system of group 4 above.

Example 2: Site-Specific Targeted Delivery of a GENE WRITER™ System into Insect Cells

This example describes a GENE WRITER™ genome editing system delivered to an insect cell at a specific target site of the genome.

In this example, the polypeptide component of the GENE WRITER™ system is derived from R2Bm of Bombyx mori, which is modified by replacing its DNA binding domain in the amino terminus of the polypeptide with a heterologous zinc-finger DNA binding domain. The zinc finger DNA binding domain is known to bind to DNA in the BmBLOS2 loci of B. mori cells (Takasu et al., insect Biochemistry and Molecular Biology 40(10): 759-765, 2010). The template RNA is RNA for the R2Bm retrotransposase from Bombyx mori containing a mutation in the reverse transcriptase domain that renders the retrotransposase inactive. Furthermore, the template RNA is modified at the 5′ end to have 180 bases of homology to the target DNA site.

B. mori insect cell lines are transfected with the following test agents:

• • 1. Scrambled RNA control
  • 2. RNA coding for polypeptide component described above
  • 3. Template RNA described above
  • 4. Combination of 2 and 3

After transfection, the cells are cultured for at least 4 days and assayed for site-specific GENE WRITING™ genome editing. Genomic DNA is isolated from the cells and PCR is conducted with primers that flank the target integration site in the genome. The PCR product is run on an agarose gel to measure the length of DNA. A PCR product of the expected length, indicative of a successful GENE WRITING™ genome editing event that inserts the sequence for the mutated R2Bm retrotransposase into the target insect cell genome, is observed only in cells that were transfected with the complete GENE WRITER™ system of group 4 above.

Example 3: Site-Specific Targeted Delivery of a GENE WRITER™ System into Mammalian Cells

This example describes a GENE WRITER™ genome editor system used to insert a heterologous sequence into a specific site of the mammalian genome.

In this example, the polypeptide of the system is the R2Bm protein from Bombyx mori and the template RNA component is RNA coding for the GFP protein and flanked at the 5′ end by the 5′ UTR and at the 3′ end by the 3′ UTR of the R2Bm retrotransposase from Bombyx mori. The GFP gene has an internal ribosomal entry site upstream of its start codon and a polyA tail downstream of its stop codon.

HEK293 cells are transfected with the following test agents:

• • 1. Scrambled RNA control
  • 2. RNA coding for the polypeptide described above
  • 3. Template RNA coding for GFP described above
  • 4. Combination of 2 and 3

After transfection, HEK293 cells are cultured for at least 4 days and then assayed for a site-specific GENE WRITING™ genome editing event. Genomic DNA is isolated from the HEK293 cells and PCR is conducted with primers that flank the R2Bm integration site in 28s rRNA genes. The PCR product is run on an agarose gel to measure the length of DNA. A PCR product of the expected length, indicative of a successful GENE WRITING™ genome editing event, is detected in cells transfected with the test agent of group 4 (complete GENE WRITER™ system). This result demonstrates that a GENE WRITING™ genome editing system can insert a novel transgene into the mammalian cell genome.

The transfected cells are cultured for a further 10 days, and after multiple cell culture passages are assayed for GFP expression via flow cytometry. The percent of cells that are GFP positive from each cell population are calculated. GFP positive cells are detected in the population of HEK293 cells that were transfected with the test agent of group 4 (complete GENE WRITER™ system). This result demonstrates that the novel transgene written into the mammalian cell genome is expressed.

Example 4: Targeted Delivery of a Gene Expression Unit into Mammalian Cells Using a GENE WRITER™ System

This example describes the making and using of a GENE WRITER™ genome editor to insert a heterologous gene expression unit into the mammalian genome.

In this example, the polypeptide of the GENE WRITER™ system is derived from the R2Bm polypeptide of Bombyx mori as modified by replacing its DNA binding domain in the amino terminus of the polypeptide with a heterologous zinc-finger DNA binding domain. The zinc finger DNA binding domain is known to bind to DNA in the AAVS1 locus of human cells (Hockemeyer et al., Nature Biotechnology 27(9): 851-857, 2009). The template RNA comprises a gene expression unit. A gene expression unit comprises at least one regulatory sequence operably linked to at least one coding sequence. In this example, the regulatory sequences include the CMV promoter and enhancer, an enhanced translation element, and a WPRE. The coding sequence is the GFP open reading frame. The gene expression unit is flanked at the 5′ end by 180 bases of homology to the target DNA site and at the 3′ end by the 3′ UTR of the R2Bm retrotransposase from Bombyx mori.

HEK293 cells are transfected with the following test agents:

• • 1. Scrambled control RNA
  • 2. RNA coding for the polypeptide component described above
  • 3. Template RNA comprising the gene expression unit (as described above)
  • 4. The complete GENE WRITER™ system comprising both (2) and (3)

After transfection, HEK293 cells are cultured for at least 4 days and assayed for site-specific GENE WRITING™ genome editing. Genomic DNA is isolated from the HEK293 cells and PCR is conducted with primers that flank the target integration site in the genome. The PCR product is run on an agarose gel to measure the length of DNA. A PCR product of the expected length, indicative of a successful GENE WRITING™ genome editing event, is detected in cells transfected with the test agent of group 4 (complete GENE WRITER™ system).

The transfected cells are cultured for a further 10 days, and after multiple cell culture passages are assayed for GFP expression via flow cytometry. The percent of cells that are GFP positive from each cell population are calculated. GFP positive cells are detected in the population of HEK293 cells that were transfected with group 4 test agent, demonstrating that a gene expression unit added into the mammalian cell genome via GENE WRITING™ genome editing is expressed.

Example 5: Targeted Delivery of a Gene Expression Unit into an Intronic Region of Mammalian Cells Using a GENE WRITER™ System

This example describes the making and use of a GENE WRITING™ genome editing system to add a heterologous sequence into an intronic region to act as a splice acceptor for an upstream exon.

The target integration site is the first intron of the albumin locus. Splicing into the first intron a new exon containing a splice acceptor site at the 5′ end and a polyA tail at the 3′ end will result in a mature mRNA containing the first natural exon of the albumin locus spliced to the new exon. Because the first exon of albumin is removed upon protein processing, the cell expressing the newly formed gene unit will secrete a mature protein comprising only the new exon.

In this example, the GENE WRITER™ genome editor polypeptide is derived from the R2Bm GENE WRITER™ genome editor of Bombyx mori as modified by replacing the DNA binding domain in the amino terminus of the polypeptide with a heterologous zinc-finger DNA binding domain. The zinc finger DNA binding domain is known to bind tightly to the albumin locus in the first intron as described in Sarma et al., Blood 126, 15: 1777-1784, 2015. The template RNA is RNA coding for EPO with a splice acceptor site immediately 5′ to the first amino acid of mature EPO (the start codon and signal peptide is removed) and a 3′ polyA tail downstream of the stop codon. The EPO RNA is further flanked at the 5′ end by 180 bases of homology to target DNA site and at the 3′ end by the 3′ UTR of the R2Bm retrotransposase from Bombyx mori.

HEK293 cells are transfected with the following test agents:

• • 1. Scrambled control RNA
  • 2. RNA coding for the polypeptide described above
  • 3. Template RNA comprising the EPO splice acceptor described above
  • 4. The complete GENE WRITER™ system comprising both (2) and (3)

After transfection, HEK293 cells are cultured for at least 4 days and assayed for site-specific GENE WRITING™ genome editing and appropriate mRNA processing. Genomic DNA is isolated from the HEK293 cells. Reverse transcription-PCR is conducted to measure the mature mRNA containing the first natural exon of the albumin locus and the new exon. The RT-PCR reaction is conducted with forward primers that bind to the first natural exon of the albumin locus and with reverse primers that bind to EPO. The RT-PCR product is run on an agarose gel to measure the length of DNA. A PCR product of the expected length is detected in cells transfected with the test agent of group 4, indicative of a successful GENE WRITING™ genome editing event and a successful splice event. This result demonstrates that a GENE WRITING™ genome editing system can add a heterologous sequence encoding a gene into an intronic region to act as a splice acceptor for the upstream exon.

The transfected cells are cultured for a further 10 days, and after multiple cell culture passages are assayed for EPO secretion in the cell supernatant. The amount of EPO in the supernatant is measured via an EPO ELISA kit. EPO is detected in HEK293 cells that were transfected with the test agent of group 4, demonstrating that a heterologous sequence can be added into an intronic region via GENE WRITING™ genome editing, to act as a splice acceptor for the upstream exon and is actively expressed.

Example 6: Targeted Delivery of R2Tg Retrotransposon to Mammalian Cells

This example describes targeted integration of the R2Tg retrotransposon element (see first row of Table 3 herein) to mammalian cells via DNA or RNA delivery.

R2Tg is an endogenous retrotransposon from the zebra finch (Taenopygia guttata). Because non-LTR R2 elements are not present in the human genome and are thought to be highly site-specific, the ability of R2Tg to accurately and efficiently integrate itself into the human genome would demonstrate the capability to perform genomic targeted integration and possibly enable human gene therapy.

In the DNA delivery method, plasmid harboring R2Tg (PLV014) was designed and synthesized such that the R2Tg element was codon optimized and flanked by its native un-translated regions (UTRs), with or without further flanking by 100 bp homology to the rDNA target locus. The R2Tg element expression was driven by the mammalian CMV promoter. Further, a lbp deletion mutant (678*) having a frameshift in the coding sequence of the retrotransposase was constructed as an inactivated control (“frameshift mutant”). Each plasmid was introduced into HEK393T cells via FuGENE® HD transfection reagent. HEK293T cells were seeded in 96-well plate, 10,000 cells/well 24 hr before transfection. On the transfection day, 0.5 μl transfection reagent and 80 ng DNA was mixed in 10 μl Opti-MEM and incubated for 15 min at room temperature. Then the transfection mixture was added to the medium of the seeded cells. 3 days after transfection, genomic DNA was extracted for retrotransposition assays.

Next, integration of the R2Tg transposase into the human genome was assessed. Based on homology to the finch genome, a putative integration site in human rDNA was tested. Advanced MISEQ™ and ddPCR assays were used to assess integration.

Bias in MISEQ™ library construction was eliminated by introducing random unique molecular indices (UMIs) into initial PCRs (FIG. 7). Nested PCR was performed by first amplifying the expected 3′ junction of R2Tg and the rDNA locus for 30 cycles. One MISEQ™ adapter, a multiplexing barcode, and an 8 bp UMI were introduced at this step. A second PCR was used to further enrich for expected products and add the second MISEQ™ adapter. Samples were sequenced on the MISEQ™ for 300 cycles. After demultiplexing, the samples were analyzed via MATLAB™. First, the UMI on each sequence was located by searching for neighboring sequence. A database of UMIs was created and next collapsed by uniqueness. For each unique read, for a search was performed for the sequence of the expected rDNA integration site and isolated sequences of aligned human genomic DNA and exogenous DNA. Exogenous DNA was then aligned to the expected integration sequence. Results of the MISEQ™ analysis pipeline are shown in FIGS. 8A-8B. Extensive unique integrations into the predicted integration site were found in cells treated with the wildtype R2Tg construct flanked by 100 bp homology to the target rDNA locus, but not with the frameshift mutant controls. Most integration events have a complete template RNA sequence integrated in the 565 bp most proximal to the integration site as demonstrated by sequencing reads that align perfectly to the expected sequence. A subset of integration events with the experimental R2Tg have either a ˜300 bp or ˜450 truncation as based upon sequencing reads that align to the expected sequence after a gap directly adjacent to the target site (FIG. 8A). More specifically, 86.17% of integrants observed were non-truncated in the 565 bp most proximal to the integration site. In contrast, FIG. 8B shows no integration events detected. Constructs without flanking rDNA homology showed insignificant integration signals near noise.

ddPCR was next performed to confirm integration and assess integration efficiency. A Taqman probe was designed to the 3′UTR portion of the R2Tg element. A forward primer was synthesized to bind directly upstream of the probe, and a reverse primer was synthesized to bind the rDNA. Therefore, amplification of the expected product across the integration junction degrades the probe and creates a fluorescent signal. ddPCR was performed on several replicate experiments of the above plasmids to determine the average copy number of the R2Tg integration event. The results of ddPCR copy number analysis (in comparison to reference gene RPP30) are shown in FIG. 9. Across several plasmid transfection conditions, average integration of 5 or more copies of R2Tg per genome at the target site when delivered with homology was noted with significant increase above control constructs. In contrast, the average copy number per genome in the frameshift mutant negative control was typically lower than 1. Insignificant signal was seen when constructs without homology were delivered to cells. The experiments collectively suggest efficient integration of the R2Tg retrotransposon into human cells at the target site.

In the RNA delivery method, R2Tg RNA (RNAV019) was designed such that the R2Tg element was codon optimized and flanked by its native untranslated regions (UTRs). More specifically, the construct includes, in order: a T7 promoter, a 5′ 28S target homology region 100 nucleotides in length, a R2Tg wild-type 5′ UTR, the R2Tg codon-optimized coding sequence, a R2Tg wild type 3′ UTR, and a 3′ 28S target homology region 100 nucleotides in length. The 100 bp 28S homology sequences were added outside of the UTRs to enhance the integration. R2Tg RNA was synthesized, and cap and polyA tail were added. The R2Tg element transcription was driven by the T7 promoter. The RNA was introduced into HEK393T cells via Lipofectamine™ RNAiMAX or TransIT®-mRNA transfection reagent with series of RNA dosages. HEK293T cells were seeded in 96-well plate 24 hr before transfection. On the transfection day, transfection reagent and RNA were mixed in 10 μl Opti-MEM, and the transfection mixture was added to the medium of the seeded cells. 3 days after transfection, genomic DNA was extracted to measure retrotransposition efficiency using ddPCR with the same design as the DNA delivery.

The results of ddPCR copy number analysis (normalized to reference gene RPP30) are shown in FIG. 12. Across several transfection conditions, the average integration was measured to be 0.01 of R2Tg copies per genome, significantly above the limit of detection. The results indicate successful integration of the R2Tg retrotransposon into human cells using an RNA delivery method.

Example 7: Targeted Delivery of a Heterologous Object Sequence Using R2Tg Retrotransposon to Mammalian Cells

This example describes the delivery of a transgene to human cells by utilizing the R2Tg retrotransposon system with multiple delivery machineries, including RNA-mediated delivery of a heterologous object sequence to human cells by utilizing the R2Tg retrotransposon system.

R2 proteins recognize their template RNA structure in untranslated regions (UTRs) of each element to form ribonucleoprotein particles, which serve as the intermediates of downstream integration into a host genome. Therefore, the decoupling of UTRs from their native context and the introduction of UTRs into alternate exogenous sequence was engineered to deliver into the genome a desired nucleic acid using R2Tg machinery.

Trans-transgene integration was tested by constructing 1) R2Tg coding sequence and 2) transgene cassette flanked by R2Tg UTR sequences and 100 bp homology to 28S rDNA into separate driver and transgene plasmids, respectively. FIG. 13 illustrates the dual plasmid system. The dual plasmids were introduced into HEK293T cells via FuGENE® HD transfection reagent at multiple driver to transgene molar ratios. In addition to the WT R2Tg driver, backbone plasmid was used as a control. HEK293T cells were seeded in 96-well plates at 10,000 cells/well 24 hr before transfection. On the transfection day, transfection reagent and plasmids were mixed in 10p Opti-MEM and incubated for 15 minutes at room temperature, then added to the medium of the seeded cells. 3 days after transfection, genomic DNA was extracted for ddPCR assays to investigate the trans-retrotransposition efficiency. FIG. 14 demonstrates the ddPCR results for conditions with excess of transgene relative to driver.

Similar to the trans-transgene delivery with plasmids, RNA delivery was performed by constructing an amplicon of the coding sequence of R2Tg preceded by the T7 promoter sequence. The constructed amplicons contained the experimental R2Tg element as well as the 1 bp deletion frameshift mutant control. Separately, an amplicon was constructed that contained exogenous sequence coding for GFP and an EGF1-alpha reporter that was flanked regions sufficient to drive integration into the genome by R2Tg. More specifically, the construct included: a T7 promoter driving transcription of the RNA, wherein the RNA comprises, from 5′ to 3′, (a) a 5′ 28S homology region of 10 nt in length, (b) a 5′ untranslated region, (c) an anti-sense TKpA polyA sequence, (d) an anti-sense heterologous object sequence that encodes GFP, (e) an anti-sense Kozak sequence, (f) an anti-sense EF1 alpha promoter, (g) a 3′ untranslated region that binds the GENE WRITER™ protein, and (h) a 3′ 28S homology region of 10 nt in length. Each RNA was transcribed via the New England Biolabs HiScribe T7 ARCA kit and purified via Zymo RNA clean and concentrator.

The resulting heterologous object RNA and R2Tg RNA (either the experiment R2Tg element or frameshift mutant) were introduced into human HEK293T cells via TransIT®-mRNA Transfection Kit at 1:1 molar ratio. HEK293T cells were seeded in 96-well plate, 40,000 cells/well 24 hr before transfection. On the transfection day, 1 μl transfection reagent and 500 ng total RNA was mixed in 10 μl Opti-MEM and incubated for 5 min at room temperature. Then the transfection mixture was added to the medium of the seeded cells. 3 days after transfection, genomic DNA was extracted for PCR assays.

Nested PCR was performed by with a first 30 rounds of PCR across the 3′ end of the expected transgene-rDNA junction, followed by 20 additional rounds of PCR amplification using an inner primer set. One of three replicates of nested PCR performed on genomic DNA extracted from cells treated with the wild-type transposase reaction produced a PCR product of the expected size (approximately 596 bp). In contrast, no PCR product was observed in genomic DNA extracted from cells treated with the frameshift-inactivated R2Tg mutant control, or no-transfection control. The PCR product was gel-purified via Zero Blunt® TOPO® PCR Cloning Kit, and the resulting colonies were Sanger sequenced. Each individual PCR product sequence was then aligned to the expected integration sequence. The fraction of PCR product sequences that align to the expected integrated heterologous object sequence is shown in FIG. 10. The majority of PCR products had the expected integrant as demonstrated by the sequencing alignment directly adjacent to the expected integration site at the right side of the alignment figure. This demonstrates RNA-mediated integration of the exogenous sequence via R2Tg machinery into human cells.

Example 8: Targeted Delivery of R2Tg Retrotransposon to Mammalian Cells

This example describes targeted integration of the R2Tg retrotransposon element to mammalian cells via DNA delivery.

Plasmid harboring R2Tg (PLV014) and control plasmid were designed and synthesized as described above in Example 6. Each plasmid was introduced into HEK393T cells via FuGENE® HD transfection reagent. HEK293T cells were seeded in 96-well plate, 10,000 cells/well 24 hr before transfection. On the transfection day, 0.5 μl transfection reagent and 80 ng DNA was mixed in 10 μl Opti-MEM and incubated for 15 min at room temperature. Then the transfection mixture was added to the medium of the seeded cells. 3 days after transfection, genomic DNA was extracted for retrotransposition assays or cells were frozen and underwent targeted locus amplification.

Target locus amplification was performed against hg38 reference human genome and the rDNA locus sequence hsul3369 (GENBANK™: U13369.1). Two independent primer sets were used to perform targeted locus amplification. Analysis with both primer sets showed that the 28S rDNA locus sequence is the only integration site detected above a 1% threshold. Thus, integration of the R2Tg transposon in mammalian cells is specific to this target site.

Example 9: Improved Trans RNA-Templated Integration into Mammalian Cells by RNA Refolding or Ratio of Driver to Template RNA

RNA templates are designed as in previous examples. Two RNAs consisting of a driver and a transgene payload are delivered to mammalian cells. To better promote folding, denaturing the payload RNA by heating to 95 C and cooling to room temperature are performed to encourage proper secondary structure formation. In some embodiments, cooling the RNA to room temperate will increase integration efficiency.

The molar ratio of transgene to driver is also varied to evaluate suitable stoichiometry of components. Integration is analyzed via ddPCR and sequencing. In some embodiments, a higher ratio of driver to transgene is used. In some embodiments, a higher ratio of transgene to driver is used.

Previous examples with cis transgene integration are similarly assayed for stoichiometry of driver to payload. Integration is analyzed via ddPCR and sequencing. In some embodiments, a higher ratio of driver transcription or translation to transgene transcription will result in higher integration efficiency. In some embodiments, a higher ratio of transgene transcription to driver transcription and translation will result in higher integration efficiency.

Example 10: Hybrid Capture Assay

A hybrid capture experiment was performed to obtain an unbiased view of the specificity of retrotransposon integration into a target site. Retrotransposon experiments were performed as in previous examples by integrating R2Tg flanked by its native UTRs and 100 bp of homology to either side of the expected R2 rDNA target. The rDNA target site had two flanking sets of 100 nucleotides identity to the corresponding native target site. The retrotransposon was delivered to human 293T cells via plasmid or mRNA. Genomic DNA was extracted after 72 hours. After extraction, each genomic DNA sample was subjected to hybrid capture according to protocol with a custom probe set (Twist). Biotinylated probes were designed such that ˜120 bp probes spanned both strands of the R2Tg coding sequence and UTRs. First, a next-generation library was created by fragmentation of the genomic DNA and ligation of sequencing adapters according to a protocol from Twist (available on the world wide web at: twistbioscience.com/ngs_protocol_custompanel_hybridcap). Next, probes were hybridized to genomic DNA libraries and the enriched samples were amplified. Final libraries were seqenced on the MISEQ™ using 300 bp paired-end reads. Custom MATLAB™ scripts were used to analyze reads. The resulting analysis is shown in FIGS. 15A and 15B for RNA delivery. Hybrid capture indicated on-target integration of R2Tg to the expected locus. With RNA delivery, 1 possible off-target with a single read was identified at an unexpected 3′ junction in the data, compared to more than 100 reads at the expected locus, indicating a specificity of greater than 100:1. At the 5′ junction, all 50 reads were at the expected locus, indicating a specificity of greater than 50:1. This experiment indicates a high specificity of integration.

Example 11: Long-Read PacBio Analysis

Long-range PCR amplification can be performed to measure integration of the desired full-length sequence into the target site in the human genome and to measure whether mutations are introduced during insertion. Retrotransposon integration experiments are performed as described in previous examples. In one example, PCR amplification is used to generate amplicons by designing one primer targeting the genomic integration site and one primer targeting the integrant sequence. In this example, these primers are designed to maximize the length of the amplified genomic locus fused with the integrant sequence. By pooling amplicons spanning both ends of the integrant and performing long-read next-generation sequencing, the fidelity of each integration is be evaluated.

In another example, hybrid capture is performed as described in a previous example but with a larger target library length during initial library generation. The resulting library is then subjected to long-read next-generation sequencing.

In some embodiments, long-read next generation sequencing will show that there are less than 10%, 5%, 2%, 1%, 0.5%, 0.2%, or 0.1% SNPs in the integrated DNA across samples. In some embodiments, long-read next generation sequencing will show that less than 10%, 5%, 2%, or 1% of integrated DNA has a SNP. In some embodiments, long-read next generation sequencing will show that less than 10%, 5%, 2%, or 1% of integrated DNA has an internal deletion. In some embodiments, long-read next generation sequencing will show that less than 10%, 5%, 2%, 1%, 0.5%, 0.2%, or 0.1% of total integrated DNA across the population is deleted. In some embodiments, long-read next generation sequencing will show that less than 10%, 5%, 2%, or 1% of integrated DNA is truncated.

Example 12: Experiment with Different Homology Lengths and Point Mutations in Homology

In this example, experiments are designed to characterize suitable lengths and starting positions of homology to the target site for efficient retrotransposon integration. Also, the homology is used to support the mechanism of integration being reverse transcription-driven.

A series of SNPs were introduced within the 100 bp downstream homology of R2Tg plasmids by modifying plasmid PLV014. The design of the SNPs is listed in FIG. 16. After the transfection, nested PCR was applied to recover the 3′ integration junction site, producing a PCR product with an expected amplicon size of about 738 bp, and the PCR product was Sanger sequenced to check whether any SNPs were incorporated. In this experiment, a lack of SNP genetic markers being incorporated into the junction sequences indicates that the integration was driven by reverse transcription. The SNP design and the sequencing result are illustrated in FIG. 16. No SNP introduction was observed for the 18 genetic markers designed, consistent with the integration of R2Tg being directed by reverse transcription.

This example also describes the evaluation different homology regions to the target site to identify shorter regions that promote efficient integration into the genome. This example describes two approaches. First, different windows of 100 bp of homology to the target site are tested, starting from bp 1-100 3′ of the target site, then testing 2-101 3′ of the target site, 3-103 3′ of the target site, and so on, through bp 30-131 3′ of the target site. Second, shorter lengths of homology to the target site sufficient for DNA integration are tested, starting with bp 0-100 3′ of the target site, then testing 0-95 3′ of the target site, 0-90 3′ of the target site, etc. through bp 0-10 3′ of the target site. After the transfection of each plasmid into 293T cells, ddPCR is used to measure the retrotransposition efficiency.

In this example, different UTR regions with different lengths are evaluated to identify shorter sequences for efficient integration into the genome. The 3′UTR is tested by dividing this 325 bp sequence into 3 regions, 1-100 bp, 101-200 bp, and 201-325 bp. Constructs of R2Tg containing each truncated 3′UTR are generated to test the integration efficiency respectively.

Example 13: Assess Whether p53 or Other Repair Pathways are Upregulated

This example describes an evaluation of the effect of exogenous R2Tg retrotranspositon on gene expression, especially tumor suppressor and DNA repair genes. An R2Tg expressing plasmid is delivered to multiple cancer cell lines, including 293T, MCF-7, and T47D. After confirmation of integration in each cell line, RNA-seq is conducted to assess the effect on gene expression profile. Gene set enrichment analysis is then applied to evaluate whether any DNA repair pathways are upregulated after retrotransposition. MCF-7 and T47D are breast cancer cell lines with wild type and mutant p53 respectively, which are be used to evaluate the relationship between p53 and retrotranspositon specifically. In some embodiments, p53 is not upregulated when a retrotransposon GENE WRITER™ integrates into the genome. In some embodiments, no DNA repair genes are upregulated when a retrotransposon GENE WRITER™ integrates into the genome. In some embodiments, no tumor suppressor genes are upregulated when a retrotransposon GENE WRITER™ integrates into the genome.

Example 14: Retrotransposition in Presence of DNA Repair Inhibitors

In this example, experiments will test the effect of different DNA repair pathways on R2Tg retrotransposition via the application of DNA repair pathway inhibitors or DNA repair pathway deficient cell lines. When applying DNA repair pathway inhibitors, PrestoBlue cell viability assay is performed first to determine the toxicity of the inhibitors and whether any normalization should be applied for following assays. SCR7 is an inhibitor for NHEJ, which is applied at a series of dilutions during R2Tg delivery. PARP protein is a nuclear enzyme that binds as homodimers to both single- and double-strand breaks. Thus, its inhibitors are be used in the test of relevant DNA repair pathways, including homologous recombination repair pathway and base excision repair pathway. The experiment procedure is the same with that of SCR7. Cell lines with deficient core proteins of nucleotide excision repair (NER) pathway are used to test the effect of NER on R2Tg retrotransposition. After the delivery of R2Tg element into the cell, ddPCR is be used to evaluate the retrotransposition in the context of inhibition of DNA repair pathways. Sequencing analysis is also be performed to evaluate whether certain DNA repair pathway plays a role in the alteration of integration junction. In some embodiments, R2Tg integration into the genome will not be decreased by the knockdown of any DNA repair pathways, suggesting that R2Tg does not rely on the host cell pathways for DNA integration.

Example 15: Retrotransposition in Fibroblasts and in T Cells

In this example, the previously performed R2Tg retrotransposition analysis of 293T cells is repeated in non-dividing cells, including fibroblast and T cells. Compared to 293T cells, non-dividing cells are sometimes more difficult to transfect with lipid reagent. Thus, nucleofection is used for the delivery of R2Tg element. The subsequent retrotransposition assay for integrating efficiency and sequencing analysis will be performed as described herein for 293T cells. In some embodiments, R2Tg integrates into the genome of fibroblasts and T cells.

Example 16: Single Cell ddPCR

In this example, a quantitative assay is used to determine the frequency of targeted genome integration at single cell level, and that information can be compared to the copy number of targeted genome integration per genome quantified from genomic DNA.

Approximately 5000 transfected cells will be collected and mixed with ddPCR reaction mixture before distributing into about 20,000 droplets, with the aim of each droplet containing one cell or no cells. ddPCR assays including 5′UTR and 3′UTR assays will be performed as described above to determine the frequency of R2 or transgene integration at single cell level. A control experiment will be performed in parallel using genomic DNA harvested from the same number of cells to determine the targeted genome integration efficiency per genome. In some embodiments, the frequency of targeted genome integration at the single cell level is calculated to be 1-80%, e.g., 25%, wherein the indicated percentage of cells have one or more copies of the transgene integrated into the desired locus.

Example 17: Single Cell Analysis Via Colony Isolation

In this example, a quantitative assay is used to determine genome integration copy number in cell colonies derived from single cell.

Single cell colonies will be isolated by colony picking up or by limited dilution and cultured in a 96 well format. When the cells reach >80% confluency, half of the cells will be frozen for backup and genomic DNA from the other half of the cells will be harvested for ddPCR. Optimized ddPCR assays including 5′UTR and 3′UTR assays will be performed as described previously to determine the frequency of R2 or transgene integration. At least 96 colonies will be screened for each R2 element with appropriate controls. The total number of colonies to be screened will be determined by single cell ddPCR data if applicable or the first set of single cell colony screen data. In some embodiments, the frequency of targeted genome integration at the single cell level will be calculated to be 1-80%, e.g., 25%, wherein the indicated percentage of cells have a single copy of the transgene integrated into the desired locus. The assay can also be used to determine the percentage of colonies that have more than one copy of the transgene integrated into the desired locus.

Example 18: DNA Binding Affinity and/or Re-Targeting

The DNA targeting module of wild-type R2 is made of a cysteine-histidine zinc finger and c-Myb transcription factor binding motifs. This N-terminal module can be substituted with different DNA binding modules such as DNA binding protein(s) (e.g., transcription factors), zinc finger(s) (e.g., natural or designed motifs), and/or nucleic acid guided, catalytically inactive endonucleases (e.g., Cas9 bound with a guide RNA (e.g., sgRNA) to form a Cas9-RNP). This DNA binding module is swapped for the naturally occurring module and, in some cases placed with a flexible linker attaching it to the RNA binding/RT module. Additionally, in some constructions, this new DNA binding module is placed in tandem with the same and/or different DNA binding modules. Furthermore, some constructions may split the GENE WRITER™ protein where one protein molecule contains the RNA binding module and the other protein contains the RT and endonuclease modules. In some embodiments, swapping of the DNA module increases specificity and/or affinity to a genomic location and in some cases allows for the specific targeting of new genomic locations.

Example 19: Assays to Measure DNA Binding Affinity

DNA binding activity of GENE WRITER™ genome editor polypeptides described herein (and DNA binding domains for the same) can be tested, e.g., as described in this example. DNA binding modules are purified by recombinantly expressing them in cells (e.g., E. coli) or they are expressed in a cell-free reactions of transcription and translation (e.g., T7 RNA polymerase+wheat germ extract). The purified DNA binding module(s) is tested for binding affinity by measuring the Kd in a binding assay (e.g., EMSA, Fluorescence anisotropy, dual-filter binding, FRET, SPR, or thermophoresis (temperature related intensity change). The protein (DNA binding module) is labeled and/or the DNA molecule is labeled with a molecule that is compatible with the above binding assays (e.g., dye, radioisotope (for example, Protein: ³⁵S-methionine, maleimide dye, DNA: ³²P end or internal label, DNA with a linked amine reacted with NHS-ester dye). The molecules are measured by changing their concentrations and fitting to a binding curve which calculates the binding affinity. In some assays, the nucleic acid sequence specificity is tested by mutational analysis of the DNA sequence or mutation to the DNA binding module by amino acid changes or alterations to protein-nucleic acid complex (e.g., Cas9-RNP DNA binding module). In some embodiments, increasing the Kd of the DNA binding module will decrease off-target insertions and, in some cases, will increase the activity of on-target sites by increasing the dwell time of the R2-RNA complex at the specific genomic location.

Example 20: Assays to Determine Global Specificity De Novo

The DNA binding module is expressed in cells (e.g., animal cells, e.g., human cells) as the DNA binding module alone, in the context of the full-length retrotransposon R2, or a control without retrotransposase. The expression of the module or retrotransposon is delivered to cells using conventional methods of delivering DNA, RNA, or protein. The complex is crosslinked (e.g., using chemical or UV light) or is not crosslinked. The cells are lysed and treated with DNase I so that only the bound DNA is protected from degradation. DNA is extracted, NGS library preparation of DNA fragments and de novo binding sites are identified, analogous to ChIP-seq or DIG-seq. In some embodiments, potential off-target sites are identified that can be followed-up to remove false-positives. In other embodiments this assay confirms the in vitro assay on the specificity of the DNA binding module to bind at its intended site and not at others.

An orthogonal assay to identify DNA binding sites in high-througput uses the method described by Boyle et al, PNAS 2017 where the DNA binding domain is tested in a cell-free setting to determine specificity along with systematic analysis of sequence mutants related to the new DNA binding module.

Example 21: Modularity of RNA Molecule

The RNA molecule binds to the R2 protein via interactions found in the reverse transcriptase module, designated as a sub-module “RNA binding”. The protein recognizes specific structures in the 5′ and/or 3′ UTRs to interact with the RNA. In some embodiments, swapping of the UTR modules increases protein interactions, changes the protein specificity to bind the UTR, stabilizes against nucleases, and/or improves cellular tolerance (e.g., leads to a reduced innate immune response). In other embodiments, addition and/or swapping of the RNA binding module of the R2 protein is compatible with the use of different sequence or ligands that are linked to the transgene and/or element module of the RNA. In some embodiments, combinations of new ligands in place of the UTRs will have better affinity to the RNA binding domain of R2 and lead to better insertion efficiency. In some embodiments, the changes to the sequence of the UTRs or changes to the base modifications of the UTRs will increase the secondary structure stability that leads to better interaction with the RNA binding module.

Example 22: Assays to Measure RNA Binding Affinity to New Sequences

New UTR modules are tested in a binding assay. In the case of new RNAs, they are synthesized either by cell-free in vitro transcription using a synthetic DNA template or by chemical synthesis of the RNA in full-length or chemical synthesis of pieces that are ligated together to form a single RNA molecule. The binding affinity of the purified UTRs are measured in a binding assay (e.g., EMSA, Fluorescence anisotropy, dual-filter binding, FRET, SPR, or thermophoresis (temperature related intensity change)). The UTR module and/or RNA binding module/RT module is detected with or without a label which is described above for labeling RNAs. Measurement of the molecules at different concentrations is performed to determine a binding affinity. In some embodiments, alterations to/swapping of the 5′ and/or 3′ UTR binding module and/or changes to the RNA binding/RT module will lead to better interactions than the wild-type R2 protein or UTR. In some embodiments, the increased interaction will lead to an increase in the efficiency of retro-transposition and in some cases increases specificity of the R2 protein to interact with the RNA.

Example 23: Alternative UTRs

While not wishing to be bound by theory, in some embodiments the UTRs act as a handle for the R2 protein to interact with the RNA which it uses as a template for RT in concert with it binding a genomic location, nicking the DNA with its endonuclease module, and then using the bound RNA as a template for RT insertion at the cleavage site in the DNA. For the UTR to keep the template in close proximity to the RT module, then the UTR modules can be substituted with different ligands that would bind to a specific RNA binding module engineered into the R2 protein. Thus, in some embodimetns, the alternative non-RNA UTR is either a protein, small molecule, or other chemical entity that is attached covalently, through protein-protein interaction, small molecule-protein interaction, or through hybridization. In some embodiments the RNA binding module binds specifically to a ligand that is not RNA that is attached to the transgene module RNA that increases the efficiency, stability, and/or rate of retro-transposition.

Example 24: Assays to Measure the Activity of UTR Constructs

Binding assays to measure affinity of R2 protein with engineered UTRs are performed as described above, e.g., for a protein-nucleic acid interaction. In cases of protein-protein or protein-small molecule interactions the assay uses a label on the RNA transgene module where the UTR module is attached.

Example 25: Targeted Genomic Integration

In this example, GENE WRITING™ technology is delivered to target cells and to non-target cells, and new DNA is integrated into the genome in target cells at a higher frequency than in non-target cells. As described in more detail below, this approach takes advantage of the non-target cell having an endogenous miRNA that the target cell does not have (or has at a lower level). The endogenous miRNA is used to reduce DNA integration in the non-target cell.

The polypeptide used is the R2Tg protein and the template RNA component is RNA coding for the GFP protein and flanked at the 5′ end by the 5′ UTR and at the 3′ end by the 3′ UTR of the R2Tg retrotransposase. The 5′ UTR is flanked by 100 bp of homology to the 5′ of R2Tg 28s rDNA target site and the 3′ UTR is flanked by 100 bp of homology to the 3′ of R2Tg 28s rDNA target site. The GFP gene is facing in the antisense direction with regard to the 5′ and 3′ UTRs and has its own promoter and polyadenylation signal.

The template RNA further comprises a microRNA recognition sequence. This microRNA recognition sequence is bound by microRNAs in the non-target cells, leading to the inhibition (e.g., degradation) of the template RNA prior to genomic integration.

In this example the target cells are hepatocytes and the non-target cells are macrophages from the hematopoietic lineage. The target cells and non-target cells are cultured separately. The template RNA and retrotransposase protein can be delivered to cells as described herein, e.g., as RNA or using viral vectors (e.g. adeno-associated viral vectors), wherein the template RNA is transcribed from viral vector DNA.

Three days after treating the cells, GFP expression and genomic integration are assayed.

GFP expression is assayed via flow cytometry. In some embodiments, GFP expression will be higher in the hepatocyte population than in the macrophage population.

Genomic integration (in terms of copy number per cell normalized to a reference gene) is assayed via droplet digital PCR using methods described herein. In some embodiments, genomic integration will be higher in the hepatocyte population than in the macrophage population.

Example 26: Testing Modularity of the DNA Binding Domain

In this example, a series of experiments were performed to test the activity of various mutant retrotransposases, as well as gaining structural knowledge about these proteins. This experiments tested flexible linkers in different locations and lengths, in order to determine if the DNA binding domain (DBD) was modular. These experiments also provide support for being able to separate the DBD from the rest of R2Tg and replacing it with any DNA targeting protein sequence. This example thus supports an understanding that the transposases described herein can withstand the tested levels of sequence divergence at a plurality of locations (e.g., in the predicted −1 RNA binding motif, in an alpha helix, and in a coil region located C-terminal to the predicted c-myb DNA binding motif, e.g., as described below) identified by structural modeling, while maintaining function.

Briefly, the two linkers (Linker A: SGSETPGTSESATPES (SEQ ID NO: 1023), and Linker B: GGGS (SEQ ID NO: 1024)) were inserted into 3 locations, noted herein as versions v1, v2, and v3. vi was located at the N-terminal side of an alpha helical region of R2Tg that preceded the predicted −1 RNA binding motif, v2 was located at the C-terminal side of an alpha helical region of R2Tg that preceded the predicted −1 RNA binding motif, and v3 was located C-terminal to a random coil region that came after the predicted c-myb DNA binding motif of R2Tg. For each of v1, v2, and v3, one of linkers A or B were added by PCR to a DNA plasmid that expressed R2Tg, thereby yielding sequences v1A (v1+linker A), v1B (v1+linker B), v1C (v1+linker C), v2A (v2+linker A), v2B (v2+linker B), and v2C (v2+linker C), as shown in Table 5 below. The insertion of the linkers was verified by Sanger sequencing and the DNA plasmids were purified for transfection.

TABLE 5
Amino acid sequences of R2Tg mutants with linkers in the DNA binding domain
(DBD)
R2Tg Mutant + Linker	Amino Acid Sequence	SEQ ID NO
R2Tg with DBD Linker	MASCPKPGPPVSAGAMSLESGLTTHSVLAIERGPNS	1017
v1A	LANSGSDFGGGGLGLPLRLLRVSVGTQTSRSDWVDL
	VSWSHPGPTSKSQQVDLVSLFPKHRVDLLSKNDQVD
	LVAQFLPSKFPPNLAENDLALLVNLEFYRSDLHVYE
	CVHFAAHWEGLSGLPEVYEQLAPQPCVGETLHSSLP
	RDSELFVPEEGSSEKESEDAPKTSPPTPGKHGLEQT
	GEEKVMVTVPDKNPPCPCCGTRVNSVLNLIEHLKVS
	HGKRGVCFRCAKCGKENSNYHSVVCHFPKCRGPETE
	KAPAGEWICEVCNRDFTTKIGLGQHKRLAHPAVRNQ
	ERIVASQPKETSNRGAHKRCWTKEEEELLIRLEAQF
	EGNKNINKLIAEHITTKTAKQISDKRRLLSRKPAEE
	PREEPGTCHHTRRAAASLRTEPEMSHHAQAEDRDNG
	PGRRPLPGRAAAGGRTMDEIRRHPDKGNGQQRPTKQ
	KSEEQLQAYYKKTLEERLSAGALNTFPRAFKQVMEG
	RDIKLVINQTAQDSGSETPGTSESATPESCFGCLES
	ISQIRTATRDKKDTVTREKHPKKPFQKWMKDRAIKK
	GNYLRFQRLFYLDRGKLAKIILDDIECLSCDIPLSE
	IYSVFKTRWETTGSFKSLGDFKTYGKADNTAFRELI
	TAKEIEKNVQEMSKGSAPGPDGITLGDVVKMDPEFS
	RTMEIFNLWLTTGKIPDMVRGCRTVLIPKSSKPDRL
	KDINNWRPITIGSILLRLFSRIVTARLSKACPLNPR
	QRGFIRAAGCSENLKLLQTIIWSAKREHRPLGVVFV
	DIAKAFDTVSHQHIIHALQQREVDPHIVGLVSNMYE
	NISTYITTKRNTHTDKIQIRVGVKQGDPMSPLLFNL
	AMDPLLCKLEESGKGYHRGQSSITAMAFADDLVLLS
	DSWENMNTNISILETFCNLTGLKTQGQKCHGFYIKP
	TKDSYTINDCAAWTINGTPLNMIDPGESEKYLGLQF
	DPWIGIARSGLSTKLDFWLQRIDQAPLKPLQKTDIL
	KTYTIPRLIYIADHSEVKTALLETLDQKIRTAVKEW
	LHLPPCTCDAILYSSTRDGGLGITKLAGLIPSVQAR
	RLHRIAQSSDDTMKCFMEKEKMEQLHKKLWIQAGGD
	RENIPSIWEAPPSSEPPNNVSTNSEWEAPTQKDKFP
	KPCNWRKNEFKKWTKLASQGRGIVNFERDKISNHWI
	QYYRRIPHRKLLTALQLRANVYPTREFLARGRQDQY
	IKACRHCDADIESCAHIIGNCPVTQDARIKRHNYIC
	ELLLEEAKKKDWVVFKEPHIRDSNKELYKPDLIFVK
	DARALVVDVTVRYEAAKSSLEEAAAEKVRKYKHLET
	EVRHLTNAKDVTFVGFPLGARGKWHQDNFKLLTELG
	LSKSRQVKMAETFSTVALFSSVDIVHMFASRARKSM
	VM
R2Tg with DBD Linker	MASCPKPGPPVSAGAMSLESGLTTHSVLAIERGPNS	1018
v1B	LANSGSDFGGGGLGLPLRLLRVSVGTQTSRSDWVDL
	VSWSHPGPTSKSQQVDLVSLFPKHRVDLLSKNDQVD
	LVAQFLPSKFPPNLAENDLALLVNLEFYRSDLHVYE
	CVHFAAHWEGLSGLPEVYEQLAPQPCVGETLHSSLP
	RDSELFVPEEGSSEKESEDAPKTSPPTPGKHGLEQT
	GEEKVMVTVPDKNPPCPCCGTRVNSVLNLIEHLKVS
	HGKRGVCFRCAKCGKENSNYHSVVCHFPKCRGPETE
	KAPAGEWICEVCNRDFTTKIGLGQHKRLAHPAVRNQ
	ERIVASQPKETSNRGAHKRCWTKEEEELLIRLEAQF
	EGNKNINKLIAEHITTKTAKQISDKRRLLSRKPAEE
	PREEPGTCHHTRRAAASLRTEPEMSHHAQAEDRDNG
	PGRRPLPGRAAAGGRTMDEIRRHPDKGNGQQRPTKQ
	KSEEQLQAYYKKTLEERLSAGALNTFPRAFKQVMEG
	RDIKLVINQTAQDGGGSCFGCLESISQIRTATRDKK
	DTVTREKHPKKPFQKWMKDRAIKKGNYLRFQRLFYL
	DRGKLAKIILDDIECLSCDIPLSEIYSVFKTRWETT
	GSFKSLGDFKTYGKADNTAFRELITAKEIEKNVQEM
	SKGSAPGPDGITLGDVVKMDPEFSRTMEIFNLWLTT
	GKIPDMVRGCRTVLIPKSSKPDRLKDINNWRPITIG
	SILLRLFSRIVTARLSKACPLNPRQRGFIRAAGCSE
	NLKLLQTIIWSAKREHRPLGVVFVDIAKAFDTVSHQ
	HIIHALQQREVDPHIVGLVSNMYENISTYITTKRNT
	HTDKIQIRVGVKQGDPMSPLLFNLAMDPLLCKLEES
	GKGYHRGQSSITAMAFADDLVLLSDSWENMNTNISI
	LETFCNLTGLKTQGQKCHGFYIKPTKDSYTINDCAA
	WTINGTPLNMIDPGESEKYLGLQFDPWIGIARSGLS
	TKLDFWLQRIDQAPLKPLQKTDILKTYTIPRLIYIA
	DHSEVKTALLETLDQKIRTAVKEWLHLPPCTCDAIL
	YSSTRDGGLGITKLAGLIPSVQARRLHRIAQSSDDT
	MKCFMEKEKMEQLHKKLWIQAGGDRENIPSIWEAPP
	SSEPPNNVSTNSEWEAPTQKDKFPKPCNWRKNEFKK
	WTKLASQGRGIVNFERDKISNHWIQYYRRIPHRKLL
	TALQLRANVYPTREFLARGRQDQYIKACRHCDADIE
	SCAHIIGNCPVTQDARIKRHNYICELLLEEAKKKDW
	VVFKEPHIRDSNKELYKPDLIFVKDARALVVDVTVR
	YEAAKSSLEEAAAEKVRKYKHLETEVRHLTNAKDVT
	FVGFPLGARGKWHQDNFKLLTELGLSKSRQVKMAET
	FSTVALFSSVDIVHMFASRARKSMVM
R2Tg with DBD Linker	MASCPKPGPPVSAGAMSLESGLTTHSVLAIERGPNS	1019
v2A	LANSGSDFGGGGLGLPLRLLRVSVGTQTSRSDWVDL
	VSWSHPGPTSKSQQVDLVSLFPKHRVDLLSKNDQVD
	LVAQFLPSKFPPNLAENDLALLVNLEFYRSDLHVYE
	CVHFAAHWEGLSGLPEVYEQLAPQPCVGETLHSSLP
	RDSELFVPEEGSSEKESEDAPKTSPPTPGKHGLEQT
	GEEKVMVTVPDKNPPCPCCGTRVNSVLNLIEHLKVS
	HGKRGVCFRCAKCGKENSNYHSVVCHFPKCRGPETE
	KAPAGEWICEVCNRDFTTKIGLGQHKRLAHPAVRNQ
	ERIVASQPKETSNRGAHKRCWTKEEEELLIRLEAQF
	EGNKNINKLIAEHITTKTAKQISDKRRLLSRKPAEE
	PREEPGTCHHTRRAAASLRTEPEMSHHAQAEDRDNG
	PGRRPLPGRAAAGGRTMDEIRRHPDKGNGQQRPTKQ
	KSEEQLQAYYKKTLEERLSAGALNTFPRAFKQVMEG
	RDIKLVINQTAQDCFGCLESISQIRSGSETPGTSES
	ATPESTATRDKKDTVTREKHPKKPFQKWMKDRAIKK
	GNYLRFQRLFYLDRGKLAKIILDDIECLSCDIPLSE
	IYSVFKTRWETTGSFKSLGDFKTYGKADNTAFRELI
	TAKEIEKNVQEMSKGSAPGPDGITLGDVVKMDPEFS
	RTMEIFNLWLTTGKIPDMVRGCRTVLIPKSSKPDRL
	KDINNWRPITIGSILLRLFSRIVTARLSKACPLNPR
	QRGFIRAAGCSENLKLLQTIIWSAKREHRPLGVVFV
	DIAKAFDTVSHQHIIHALQQREVDPHIVGLVSNMYE
	NISTYITTKRNTHTDKIQIRVGVKQGDPMSPLLFNL
	AMDPLLCKLEESGKGYHRGQSSITAMAFADDLVLLS
	DSWENMNTNISILETFCNLTGLKTQGQKCHGFYIKP
	TKDSYTINDCAAWTINGTPLNMIDPGESEKYLGLQF
	DPWIGIARSGLSTKLDFWLQRIDQAPLKPLQKTDIL
	KTYTIPRLIYIADHSEVKTALLETLDQKIRTAVKEW
	LHLPPCTCDAILYSSTRDGGLGITKLAGLIPSVQAR
	RLHRIAQSSDDTMKCFMEKEKMEQLHKKLWIQAGGD
	RENIPSIWEAPPSSEPPNNVSTNSEWEAPTQKDKFP
	KPCNWRKNEFKKWTKLASQGRGIVNFERDKISNHWI
	QYYRRIPHRKLLTALQLRANVYPTREFLARGRQDQY
	IKACRHCDADIESCAHIIGNCPVTQDARIKRHNYIC
	ELLLEEAKKKDWVVFKEPHIRDSNKELYKPDLIFVK
	DARALVVDVTVRYEAAKSSLEEAAAEKVRKYKHLET
	EVRHLTNAKDVTFVGFPLGARGKWHQDNFKLLTELG
	LSKSRQVKMAETFSTVALFSSVDIVHMFASRARKSM
	VM
R2Tg with DBD Linker	MASCPKPGPPVSAGAMSLESGLTTHSVLAIERGPNS	1020
v2B	LANSGSDFGGGGLGLPLRLLRVSVGTQTSRSDWVDL
	VSWSHPGPTSKSQQVDLVSLFPKHRVDLLSKNDQVD
	LVAQFLPSKFPPNLAENDLALLVNLEFYRSDLHVYE
	CVHFAAHWEGLSGLPEVYEQLAPQPCVGETLHSSLP
	RDSELFVPEEGSSEKESEDAPKTSPPTPGKHGLEQT
	GEEKVMVTVPDKNPPCPCCGTRVNSVLNLIEHLKVS
	HGKRGVCFRCAKCGKENSNYHSVVCHFPKCRGPETE
	KAPAGEWICEVCNRDFTTKIGLGQHKRLAHPAVRNQ
	ERIVASQPKETSNRGAHKRCWTKEEEELLIRLEAQF
	EGNKNINKLIAEHITTKTAKQISDKRRLLSRKPAEE
	PREEPGTCHHTRRAAASLRTEPEMSHHAQAEDRDNG
	PGRRPLPGRAAAGGRTMDEIRRHPDKGNGQQRPTKQ
	KSEEQLQAYYKKTLEERLSAGALNTFPRAFKQVMEG
	RDIKLVINQTAQDCFGCLESISQIRGGGSTATRDKK
	DTVTREKHPKKPFQKWMKDRAIKKGNYLRFQRLFYL
	DRGKLAKIILDDIECLSCDIPLSEIYSVFKTRWETT
	GSFKSLGDFKTYGKADNTAFRELITAKEIEKNVQEM
	SKGSAPGPDGITLGDVVKMDPEFSRTMEIFNLWLTT
	GKIPDMVRGCRTVLIPKSSKPDRLKDINNWRPITIG
	SILLRLFSRIVTARLSKACPLNPRQRGFIRAAGCSE
	NLKLLQTIIWSAKREHRPLGVVFVDIAKAFDTVSHQ
	HIIHALQQREVDPHIVGLVSNMYENISTYITTKRNT
	HTDKIQIRVGVKQGDPMSPLLFNLAMDPLLCKLEES
	GKGYHRGQSSITAMAFADDLVLLSDSWENMNTNISI
	LETFCNLTGLKTQGQKCHGFYIKPTKDSYTINDCAA
	WTINGTPLNMIDPGESEKYLGLQFDPWIGIARSGLS
	TKLDFWLQRIDQAPLKPLQKTDILKTYTIPRLIYIA
	DHSEVKTALLETLDQKIRTAVKEWLHLPPCTCDAIL
	YSSTRDGGLGITKLAGLIPSVQARRLHRIAQSSDDT
	MKCFMEKEKMEQLHKKLWIQAGGDRENIPSIWEAPP
	SSEPPNNVSTNSEWEAPTQKDKFPKPCNWRKNEFKK
	WTKLASQGRGIVNFERDKISNHWIQYYRRIPHRKLL
	TALQLRANVYPTREFLARGRQDQYIKACRHCDADIE
	SCAHIIGNCPVTQDARIKRHNYICELLLEEAKKKDW
	VVFKEPHIRDSNKELYKPDLIFVKDARALVVDVTVR
	YEAAKSSLEEAAAEKVRKYKHLETEVRHLTNAKDVT
	FVGFPLGARGKWHQDNFKLLTELGLSKSRQVKMAET
	FSTVALFSSVDIVHMFASRARKSMVM
R2Tg with DBD Linker	MASCPKPGPPVSAGAMSLESGLTTHSVLAIERGPNS	1021
v3A	LANSGSDFGGGGLGLPLRLLRVSVGTQTSRSDWVDL
	VSWSHPGPTSKSQQVDLVSLFPKHRVDLLSKNDQVD
	LVAQFLPSKFPPNLAENDLALLVNLEFYRSDLHVYE
	CVHFAAHWEGLSGLPEVYEQLAPQPCVGETLHSSLP
	RDSELFVPEEGSSEKESEDAPKTSPPTPGKHGLEQT
	GEEKVMVTVPDKNPPCPCCGTRVNSVLNLIEHLKVS
	HGKRGVCFRCAKCGKENSNYHSVVCHFPKCRGPETE
	KAPAGEWICEVCNRDFTTKIGLGQHKRLAHPAVRNQ
	ERIVASQPKETSNRGAHKRCWTKEEEELLIRLEAQF
	EGNKNINKLIAEHITTKTAKQISDKRRLLSRKPAEE
	PREEPGTCHHTRRAASGSETPGTSESATPESASLRT
	EPEMSHHAQAEDRDNGPGRRPLPGRAAAGGRTMDEI
	RRHPDKGNGQQRPTKQKSEEQLQAYYKKTLEERLSA
	GALNTFPRAFKQVMEGRDIKLVINQTAQDCFGCLES
	ISQIRTATRDKKDTVTREKHPKKPFQKWMKDRAIKK
	GNYLRFQRLFYLDRGKLAKIILDDIECLSCDIPLSE
	IYSVFKTRWETTGSFKSLGDFKTYGKADNTAFRELI
	TAKEIEKNVQEMSKGSAPGPDGITLGDVVKMDPEFS
	RTMEIFNLWLTTGKIPDMVRGCRTVLIPKSSKPDRL
	KDINNWRPITIGSILLRLFSRIVTARLSKACPLNPR
	QRGFIRAAGCSENLKLLQTIIWSAKREHRPLGVVFV
	DIAKAFDTVSHQHIIHALQQREVDPHIVGLVSNMYE
	NISTYITTKRNTHTDKIQIRVGVKQGDPMSPLLFNL
	AMDPLLCKLEESGKGYHRGQSSITAMAFADDLVLLS
	DSWENMNTNISILETFCNLTGLKTQGQKCHGFYIKP
	TKDSYTINDCAAWTINGTPLNMIDPGESEKYLGLQF
	DPWIGIARSGLSTKLDFWLQRIDQAPLKPLQKTDIL
	KTYTIPRLIYIADHSEVKTALLETLDQKIRTAVKEW
	LHLPPCTCDAILYSSTRDGGLGITKLAGLIPSVQAR
	RLHRIAQSSDDTMKCFMEKEKMEQLHKKLWIQAGGD
	RENIPSIWEAPPSSEPPNNVSTNSEWEAPTQKDKFP
	KPCNWRKNEFKKWTKLASQGRGIVNFERDKISNHWI
	QYYRRIPHRKLLTALQLRANVYPTREFLARGRQDQY
	IKACRHCDADIESCAHIIGNCPVTQDARIKRHNYIC
	ELLLEEAKKKDWVVFKEPHIRDSNKELYKPDLIFVK
	DARALVVDVTVRYEAAKSSLEEAAAEKVRKYKHLET
	EVRHLTNAKDVTFVGFPLGARGKWHQDNFKLLTELG
	LSKSRQVKMAETFSTVALFSSVDIVHMFASRARKSM
	VM
R2Tg with DBD Linker	MASCPKPGPPVSAGAMSLESGLTTHSVLAIERGPNS	1022
v3B	LANSGSDFGGGGLGLPLRLLRVSVGTQTSRSDWVDL
	VSWSHPGPTSKSQQVDLVSLFPKHRVDLLSKNDQVD
	LVAQFLPSKFPPNLAENDLALLVNLEFYRSDLHVYE
	CVHFAAHWEGLSGLPEVYEQLAPQPCVGETLHSSLP
	RDSELFVPEEGSSEKESEDAPKTSPPTPGKHGLEQT
	GEEKVMVTVPDKNPPCPCCGTRVNSVLNLIEHLKVS
	HGKRGVCFRCAKCGKENSNYHSVVCHFPKCRGPETE
	KAPAGEWICEVCNRDFTTKIGLGQHKRLAHPAVRNQ
	ERIVASQPKETSNRGAHKRCWTKEEEELLIRLEAQF
	EGNKNINKLIAEHITTKTAKQISDKRRLLSRKPAEE
	PREEPGTCHHTRRAAGGGSASLRTEPEMSHHAQAED
	RDNGPGRRPLPGRAAAGGRTMDEIRRHPDKGNGQQR
	PTKQKSEEQLQAYYKKTLEERLSAGALNTFPRAFKQ
	VMEGRDIKLVINQTAQDCFGCLESISQIRTATRDKK
	DTVTREKHPKKPFQKWMKDRAIKKGNYLRFQRLFYL
	DRGKLAKIILDDIECLSCDIPLSEIYSVFKTRWETT
	GSFKSLGDFKTYGKADNTAFRELITAKEIEKNVQEM
	SKGSAPGPDGITLGDVVKMDPEFSRTMEIFNLWLTT
	GKIPDMVRGCRTVLIPKSSKPDRLKDINNWRPITIG
	SILLRLFSRIVTARLSKACPLNPRQRGFIRAAGCSE
	NLKLLQTIIWSAKREHRPLGVVFVDIAKAFDTVSHQ
	HIIHALQQREVDPHIVGLVSNMYENISTYITTKRNT
	HTDKIQIRVGVKQGDPMSPLLFNLAMDPLLCKLEES
	GKGYHRGQSSITAMAFADDLVLLSDSWENMNTNISI
	LETFCNLTGLKTQGQKCHGFYIKPTKDSYTINDCAA
	WTINGTPLNMIDPGESEKYLGLQFDPWIGIARSGLS
	TKLDFWLQRIDQAPLKPLQKTDILKTYTIPRLIYIA
	DHSEVKTALLETLDQKIRTAVKEWLHLPPCTCDAIL
	YSSTRDGGLGITKLAGLIPSVQARRLHRIAQSSDDT
	MKCFMEKEKMEQLHKKLWIQAGGDRENIPSIWEAPP
	SSEPPNNVSTNSEWEAPTQKDKFPKPCNWRKNEFKK
	WTKLASQGRGIVNFERDKISNHWIQYYRRIPHRKLL
	TALQLRANVYPTREFLARGRQDQYIKACRHCDADIE
	SCAHIIGNCPVTQDARIKRHNYICELLLEEAKKKDW
	VVFKEPHIRDSNKELYKPDLIFVKDARALVVDVTVR
	YEAAKSSLEEAAAEKVRKYKHLETEVRHLTNAKDVT
	FVGFPLGARGKWHQDNFKLLTELGLSKSRQVKMAET
	FSTVALFSSVDIVHMFASRARKSMVM

HEK293T cells were plated in 96-well plates and grown overnight at 37° C., 5% CO2. The HEK293T cells were transfected with plasmids that expressed R2Tg (wild-type), R2 endonuclease mutant, and linker mutants. The transfection was carried out using the Fugene HID transfection reagent according to the manufacturer recommendations, where each well received 80 ng of plasmid DNA and 0.5 μL of transfection reagent. All transfections were performed in duplicate and the cells were incubated for 72 h prior to genomic DNA extraction.

Activity of the mutants was measured by a ddPCR assay that quantified the copy number of R2Tg integration per genome. The 5′ and 3′ junctions were quantified by generating two different amplicons at each end.

v3 (near the c-myb binding motif in the DBD) decreased integration activity with either linker A or B. v1 (N-terminal to the alpha helix preceding the −1 RNA binding motif) had comparable activity to the wild-type when used with linker A (16 AA) versus the shorter linker B (4 AA). This could be related to amino acid selection, length, or three-dimensional structure. v2 (C-terminal to the alpha helix preceding the −1 RNA binding motif) did not tolerate linker A; however, linker B had activity that was comparable and slightly better than the wild-type. v1 and v2 may therefore be considered preferred locations to add a linker that can separate R2Tg's DNA binding domain and the rest of the protein.

Example 27: Long-Read Sequencing to Determine Integration Fidelity

Retrotransposon integration experiments were performed as described in previous examples. In one example, PCR amplification was used to generate amplicons by designing one primer targeting the genomic integration site and one primer targeting the integrant sequence. In this example, these primers were designed to maximize the length of the amplified genomic locus fused with the integrant sequence. By pooling amplicons spanning both ends of the integrant and performing long-read next-generation sequencing, the fidelity of each integration was evaluated.

A cis construct of R2Tg was integrated into 293T cells via plasmid transfection as described herein. Amplicons spanning each end of the integrations were generated with flanking randomized UMIs to control for PCR bias. These amplicons were sequenced with PacBio next-generation sequencing. The resulting sequences were collapsed to remove reads with identical UMIs. By aligning unique reads, a coverage plot was constructed as shown in FIGS. 20A-20B. Sequence coverage largely shows uniform coverage across amplicons, indicating significant fidelity of integration. An associated reverse-transcriptase deficient mutant control produced no signal. Internal deletions were also analyzed in FIGS. 21A-21B. Internal deletions were generally low relative to overall unique read counts, with some clustering at the 5′ junction of rDNA-R2Tg.

In another example, hybrid capture may be performed as described in a previous example but with a larger target library length during initial library generation. The resulting library can then be subjected to long-read next-generation sequencing.

Example 28: Targeted Delivery of R2Gfo and R4Al Retrotransposon to Mammalian Cells

This example describes targeted integration of the R2Gfo and R4Al retrotransposon elements to mammalian cells via DNA delivery.

In one example, we assayed the full R2 element R2-1_GFo (Repbase; Kojima et al PLoS One 11, e0163496 (2015)) from the medium ground finch, Geospiza fortis (“R2GFo”). In another example, we assayed the full R4 element R4_AL (Repbase; Burke et al Nucleic Acids Res. 23, 4628-34 (1995)) from the large roundworm, Ascaris lumbricoides (“R4Al”). Because non-LTR R2 and R4 elements are not present in the human genome and are thought to be highly site-specific, the ability of retrotransposons to accurately and efficiently integrate itself into the human genome would demonstrate the capability to perform genomic targeted integration.

Plasmids harboring R2Gfo (PLV033) or R4Al (PLV462) were designed for cis integration of the R2Gfo or R4Al elements as in previous examples. Plasmids were synthesized such that the wildtype element was flanked by its native un-translated regions (UTRs) and 100 bp of homology to its rDNA target (FIG. 22). The element expression was driven by the mammalian CMV promoter. We introduced each plasmid into HEK393T cells using the FuGENE® HD transfection reagent. HEK293T cells were seeded in 96-well plates at 10,000 cells/well 24 hours before transfection. On the transfection day, 0.5 μl transfection reagent and 80 ng DNA was mixed in 10 μl Opti-MEM and incubated for 15 minutes at room temperature. The transfection mixture was then added to the medium of the seeded cells. Three days after transfection, genomic DNA was extracted for retrotransposition assays. R2Tg was also delivered in parallel in the same format to serve as a comparison.

ddPCR was performed to confirm integration and assess integration efficiency. A Tagman probe was designed to the 3′UTR portion of each element. A forward primer was synthesized to bind directly upstream of the probe, and a reverse primer was synthesized to bind the rDNA. Thus, amplification of the expected product across the integration junction would degrade the probe and create a fluorescent signal. The results of the ddPCR copy number analysis (in comparison to reference gene RPP30) are shown in FIG. 23. R2Gfo integration achieved a mean copy number of 0.21 integrants/genome in this experiment. R4Al achieved a mean copy number of 0.085 integrants/genome.

Example 29: Integration of Retrotransposons into Human Fibroblasts

This example describes the cis integration of R2Tg into human fibroblasts. Briefly, a plasmid designed to integrate R2Tg in cis was synthesized such that R2Tg was flanked by its native UTRs and homologous sequence to its rDNA target as in previous examples. 0.5 μg PLV014 (wild-type) and PLV072 (EN mutant) plasmids were transfected into 100,000 human dermal fibroblasts isolated from neonatal foreskin (HDFn, C0045C, ThermoFisher Scientific) respectively using the Neon transfection system. Two programs were performed, each in duplicate. The setting for Program 1 was 1700V pulse voltage, 20 ms pulse width, and 1 pulse number. The setting for Program 2 was 1400V pulse voltage, 20 ms pulse width, and 2 pulse number. Both programs achieved 95% transfection efficiency measured using plasmid encoding the EGFP. Three days post transfection, genomic DNA was extracted for the ddPCR assay. ddPCR was performed to confirm integration and assess integration efficiency. A Tagman probe was designed to the 3′ UTR portion of the R2Tg element. A forward primer was synthesized to bind directly upstream of the probe, and a reverse primer was synthesized to bind the rDNA. Thus, amplification of the expected product across the integration junction would degrade the probe and create a fluorescent signal. The results of ddPCR copy number analysis (in comparison to reference gene RPP30) are shown in FIG. 24. Wild-type (WT) R2Tg integration achieved a mean copy number of 0.036 integrants/genome in this experiment, significantly higher than a control R2Tg plasmid with a point mutation abolishing endonuclease activity (EN).

Example 30: Evaluation of DNA Damage Response Upon Retrotransposon Transfection

DNA damage (e.g., resulting from DSB formation or replication fork collapse) leads to the activation of p53, which among many other transcriptional responses, leads to the upregulation of p21, resulting in cell cycle arrest or apoptosis. Genome editing using CRISRP/Cas9 has been shown to activate p53 and p21, which is a potential safety and efficacy problem for CRISPR/based therapeutics. To establish whether R2Tg delivery to the cell leads to activation of p53 and p21, U2OS cells were seeded at a density of 4×10⁴ cells/well and transfected 24 hours later using the Fugene HD and Lipofectamine reagents with either 500 ng of R2Tg-WT plasmid or 500 ng of R2Tg-EN (a variant of R2Tg with a mutation in the endonuclease (EN) domain, rendering R2Tg inactive). To control for transfection efficiency, U2OS cells were also transfected with a plasmid expressing GFP. Lastly, as a positive control for p53 and p21 activation, U2OS cells were treated with one of the DNA damage-inducing agents etoposide (20 μM) or bleomycin (10 μg/ml). The U2OS cells were collected 24 hours after transfection/treatment. Protein lysates were prepared in RIPA buffer and run on an SDS-PAGE gel, followed by transfer to nitrocellulose, followed by probing with antibodies against p53 and p21, as well as Actin and Vinculin. As shown in FIG. 25, no R2Tg-induced upregulation of p53 or p21 above the GFP plasmid control was detected in either transfection condition.

LENGTHY TABLES
The patent application contains a lengthy table section. A copy of the table is available in electronic form from the USPTO web site (). An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

Claims

1. A system for modifying DNA, the system comprising: (a) a polypeptide or a nucleic acid encoding the polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain, wherein (i) is derived from a retrovirus; and(b) a template RNA or a DNA encoding the template RNA, wherein the template RNA comprises (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence comprising a sequence that encodes a polypeptide.

2. The system of claim 1, wherein the endonuclease domain contains DNA binding functionality.

3. The system of claim 1, wherein the polypeptide comprises a Cas9, Cpf1, or other CRISPR-related protein.

4. The system of claim 1, wherein (a) and (b) are separate RNAs.

5. A method of modifying a target DNA strand in a cell, tissue or subject, the method comprising administering the system of claim 1 to the cell, tissue or subject, thereby modifying the target DNA strand.

6. A system for modifying DNA, the system comprising: (a) a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain, (ii) an endonuclease domain, and (iii) a DNA binding domain comprising zinc-finger element, or a functional fragment thereof; a TAL effector element, or a functional fragment thereof, or a Myb domain; and(b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence,wherein (a) and (b) are separate RNAs.

7. The system of claim 6, wherein (i) and (ii) are derived from a retrotransposase.

8. The system of claim 7, wherein (i) and (ii) are derived from an RLE-type retrotransposase.

9. The system of claim 6, wherein at least one of (i) or (ii) is heterologous.

10. A method of modifying a target DNA strand in a cell, tissue or subject, the method comprising administering the system of claim 6 to the cell, tissue or subject, thereby modifying the target DNA strand.

11. A system for modifying DNA comprising: (a) a polypeptide or a nucleic acid encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain, wherein (i) and (ii) are derived from a retrotransposase, and wherein the polypeptide has an activity at 37° C. that is no less than 70% of its activity at 25° C. under otherwise similar conditions; and(b) a template RNA (or DNA encoding the template RNA) comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence.

12. The system of claim 11, wherein the polypeptide is derived from an avian retrotransposase.

13. A method of modifying a target DNA strand in a cell, tissue or subject, the method comprising administering the system of claim 11 to the cell, tissue or subject, thereby modifying the target DNA strand.

14. A method of modifying a target DNA strand in a cell, tissue or subject, the method comprising administering a system for modifying DNA to the cell, tissue or subject, thereby modifying the target DNA strand; wherein the system for modifying DNA comprises:(a) a first engineered RNA encoding a polypeptide, wherein the polypeptide comprises (i) a reverse transcriptase domain and (ii) an endonuclease domain, and wherein each of (i) and (ii) are derived from a retrotransposase; and(b) a second engineered RNA comprising a template RNA, wherein the template RNA comprises (i) a sequence that binds the encoded polypeptide, and (ii) a heterologous object sequence; andwherein (a) and (b) are separate RNAs.

15. The method of claim 14, wherein: (i) the template RNA further comprises a sequence comprising at least 20 nucleotides of at least 80% identity to a target DNA;(ii) the target DNA is a genomic safe harbor (GSH) site; and/or(iii) the sequence that binds the polypeptide comprises one or both of a 3′ untranslated region and a 5′ untranslated region.

16. The method of claim 14, wherein the template RNA comprises: (iii) at least 3 bases of identity to a target DNA at the 3′ end of the template RNA, and (iv) at least 3 bases of identity to the target DNA at the 5′ end of the template RNA.

17. The method of claim 14, wherein the heterologous object sequence: (i) encodes an enzyme, a membrane protein, a blood factor, an intracellular protein, an extracellular protein, a structural protein, a signaling protein, a regulatory protein, a transport protein, or a motor protein;(ii) encodes a therapeutic polypeptide or fragment thereof; or(iii) comprises a non-coding sequence or a regulatory sequence.

18. The method of claim 14, wherein the polypeptide further comprises one or both of a nuclear localization signal and a nucleolar localization signal.

19. The method of claim 14, wherein the system: (A) comprises: (i) only RNA, or comprises more RNA than DNA by an RNA:DNA ratio of at least 10:1, 20:1, 30:1, 40:1, 50:1, 60:1, 70:1, 80:1, 90:1, or 100:1; and/or(ii) no more than 1%, 0.5%, 0.2%, 0.1%, 0.05%, 0.02%, or 0.01% DNA by mass or by molar amount of nucleic acid; and/or(B) is capable of modifying DNA in the absence of homologous recombination activity.

20. The method of claim 14, wherein the template RNA does not encode a reverse transcriptase and/or an endonuclease.